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Items where Faculty / School / Research Centre / Research Groups is "Molecular Virology and Entomology Research Group"

Items where Faculty / School / Research Centre / Research Groups is "Molecular Virology and Entomology Research Group"

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AB SOLiD accessory chromosome Aegilops tauschii agro-ecological regions Alternaria alternata Alternaria section Alternaria Alternariaarborescensspeciescomplex Alternariafruitspot Alternarialeafblotch Arabidopsis thaliana autoSNP BAC Badna-PCR Badnavirus Bayoud disease Bemisia tabaci Betaflexiviridae biofuels bioinformatics biosecurity biotroph BNG map Capacity building cassava brown streak viruses cell cycle cell suspension culture cell wall 25 proteins Centromere Cereals Chromsosomes closed‑tube reverse transcription loop‑mediated isothermal amplification (CT-RT-LAMP) COI1 Complete genome crown rot cryptic species CTG clade yeast database date palm denaturing gradient gel electrophoresis (DGGE) detection diagnostic assay Diagnostics Dioscorea Dioscorea rotundata Dioscorea spp. discovery diversity DNA extraction dose response early virus detection effector effectors endogenous badnaviral elements Endogenous Dioscorea bacilliform virus Endogenous pararetrovirus Endogenous pararetrovirus (EPRV) Episomal badnavirus Evolution Flow sorting Food security Fragaria Fusarium oxysporum gene flow genetic differentiation genetic variation genome genome diversity genome plasticity Genome sequencing genomic instability genomics genotyping by sequencing haplotype high-throughput sequencing horticulture host-plants HTS Illumina In vitro culture Integration Ion Torrent isothermal amplification jasmonate LAMP leaf beetle lineage specific linkage map Maize streak virus Markers microsatellites mitochondrial DNA mitogenome Molecular biology MSV multiplex PCR mycology next-generation sequencing Next-generation sequencing – SASSY – BAC – Assembly – 7DS – Triticum aestivum – Saccharum spp oomycete Optical mapping Oxford nanopore Pacific biosciences pandemic pangenome Pathogenic fungi Pathogenicity of plant pathogens Phoenix dactylifera phylogenomics Phylogeny Physical Map phytopathology Phytophthora plant pathogen Plant pathology plant virus plant-pathogen polygenic Polyploidy Potyvirus primary metabolism quantitative trait loci (QTLs) rapid diagnosis Recombination Reverse transcriptase recombinase polymerase amplification (RT-RPA) RNA-Seq Roche 454 Rolling circle amplification RT-LAMP Rubus seed systems Sequence diversity Sequencing single nucleotide polymorphism (SNP) single nucleotide polymorphisms Small-spored Alternaria Sphaerotheca macularis SSA3 stress–signalling Sub-Saharan Africa surveillance tebuconazole Thjileria Parva transposons Triticum aestivum Uganda vaccine development virus detection virus diagnostics West Africa wheat whitefly species Yam Yam mosaic virus YMV
Number of items at this level: 206.

AB SOLiD

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

accessory chromosome

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

Aegilops tauschii

Tulpová, Zuzana, Luo, Ming-Cheng, Toegelová, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michaël, Bartoš, Jan, Hajdúch, Marián, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology, 48. pp. 12-19. ISSN 1871-6784 (Print), 1876-4347 (Online) (doi:https://doi.org/10.1016/j.nbt.2018.03.003)

agro-ecological regions

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

Alternaria alternata

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Alternaria section Alternaria

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Alternariaarborescensspeciescomplex

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Alternariafruitspot

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Alternarialeafblotch

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Arabidopsis thaliana

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

autoSNP

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

BAC

Tulpová, Zuzana, Luo, Ming-Cheng, Toegelová, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michaël, Bartoš, Jan, Hajdúch, Marián, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology, 48. pp. 12-19. ISSN 1871-6784 (Print), 1876-4347 (Online) (doi:https://doi.org/10.1016/j.nbt.2018.03.003)

Badna-PCR

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Badnavirus

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105. pp. 54-66. ISSN 0885-5765 (Print), 1096-1178 (Online) (doi:https://doi.org/10.1016/j.pmpp.2018.06.003)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Bayoud disease

Khayi, Slimane ORCID: 0000-0001-8033-2117 , Armitage, Andrew ORCID: 0000-0002-0610-763X , El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: 0000-0003-1067-1652 , Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: 0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:https://doi.org/10.1080/23802359.2021.1978894)

Bemisia tabaci

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

Betaflexiviridae

Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

biofuels

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)

bioinformatics

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

biosecurity

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Tomlinson, Jenny, Onkokesung, Nawaporn, Sommer, Sarah, Mrisho, Latifa, Legg, James, Silva, Ian P., Gutierrez-Vazquez, Yaiza, Howard, Thomas P., Laverick, Alex, Hossain, Oindrila, Wei, Qingshan, M. Gold, Kaitlin and Boonham, Neil (2021) Plant pest surveillance: from satellites to molecules. Emerging Topics in Life Sciences, 5 (2). pp. 275-287. ISSN 2397-8554 (Print), 2397-8562 (Online) (doi:https://doi.org/10.1042/ETLS20200300)

biotroph

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

BNG map

Tulpová, Zuzana, Luo, Ming-Cheng, Toegelová, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michaël, Bartoš, Jan, Hajdúch, Marián, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology, 48. pp. 12-19. ISSN 1871-6784 (Print), 1876-4347 (Online) (doi:https://doi.org/10.1016/j.nbt.2018.03.003)

Capacity building

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

cassava brown streak viruses

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: 0000-0002-3952-1562 , Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports, 14:12438. pp. 1-11. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-024-62249-y)

cell cycle

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

cell suspension culture

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

cell wall 25 proteins

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

Centromere

Tulpová, Zuzana, Luo, Ming-Cheng, Toegelová, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michaël, Bartoš, Jan, Hajdúch, Marián, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology, 48. pp. 12-19. ISSN 1871-6784 (Print), 1876-4347 (Online) (doi:https://doi.org/10.1016/j.nbt.2018.03.003)

Cereals

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

Chromsosomes

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

closed‑tube reverse transcription loop‑mediated isothermal amplification (CT-RT-LAMP)

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

COI1

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

Complete genome

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

crown rot

Armitage, Andrew ORCID: 0000-0002-0610-763X , Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)

cryptic species

Armitage, Andrew ORCID: 0000-0002-0610-763X , Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)

CTG clade yeast

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)

database

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

Visendi, Paul, Ng'ang'a, Wanjiku, Bulimo, Wallace, Bishop, Richard, Ochanda, James and de Villiers, Etienne P. (2011) TparvaDB: a database to support Theileria parva vaccine development. Database, 2011. bar015-bar015. ISSN 1758-0463 (Online) (doi:https://doi.org/10.1093/database/bar015)

date palm

Khayi, Slimane ORCID: 0000-0001-8033-2117 , Armitage, Andrew ORCID: 0000-0002-0610-763X , El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: 0000-0003-1067-1652 , Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: 0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:https://doi.org/10.1080/23802359.2021.1978894)

denaturing gradient gel electrophoresis (DGGE)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

detection

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

diagnostic assay

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

Diagnostics

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Tomlinson, Jenny, Onkokesung, Nawaporn, Sommer, Sarah, Mrisho, Latifa, Legg, James, Silva, Ian P., Gutierrez-Vazquez, Yaiza, Howard, Thomas P., Laverick, Alex, Hossain, Oindrila, Wei, Qingshan, M. Gold, Kaitlin and Boonham, Neil (2021) Plant pest surveillance: from satellites to molecules. Emerging Topics in Life Sciences, 5 (2). pp. 275-287. ISSN 2397-8554 (Print), 2397-8562 (Online) (doi:https://doi.org/10.1042/ETLS20200300)

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

Dioscorea

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

Dioscorea rotundata

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Dioscorea spp.

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105. pp. 54-66. ISSN 0885-5765 (Print), 1096-1178 (Online) (doi:https://doi.org/10.1016/j.pmpp.2018.06.003)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

discovery

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

diversity

Khayi, Slimane ORCID: 0000-0001-8033-2117 , Armitage, Andrew ORCID: 0000-0002-0610-763X , El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: 0000-0003-1067-1652 , Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: 0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:https://doi.org/10.1080/23802359.2021.1978894)

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

DNA extraction

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

dose response

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

early virus detection

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: 0000-0002-3952-1562 , Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports, 14:12438. pp. 1-11. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-024-62249-y)

effector

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

effectors

Armitage, Andrew ORCID: 0000-0002-0610-763X , Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)

endogenous badnaviral elements

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

Endogenous Dioscorea bacilliform virus

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Endogenous pararetrovirus

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Endogenous pararetrovirus (EPRV)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Episomal badnavirus

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Evolution

Berkman, Paul J., Visendi, Paul, Lee, Hong C., Stiller, Jiri, Manoli, Sahana, Lorenc, Michał T., Lai, Kaitao, Batley, Jacqueline, Fleury, Delphine, Šimková, Hana, Kubaláková, Marie, Weining, Song, Doležel, Jaroslav and Edwards, David (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal, 11 (5). pp. 564-571. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12044)

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

Flow sorting

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

Food security

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

Fragaria

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

Fusarium oxysporum

Khayi, Slimane ORCID: 0000-0001-8033-2117 , Armitage, Andrew ORCID: 0000-0002-0610-763X , El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: 0000-0003-1067-1652 , Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: 0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:https://doi.org/10.1080/23802359.2021.1978894)

gene flow

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

genetic differentiation

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

genetic variation

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

genome

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

genome diversity

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

genome plasticity

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)

Genome sequencing

Berkman, Paul J., Visendi, Paul, Lee, Hong C., Stiller, Jiri, Manoli, Sahana, Lorenc, Michał T., Lai, Kaitao, Batley, Jacqueline, Fleury, Delphine, Šimková, Hana, Kubaláková, Marie, Weining, Song, Doležel, Jaroslav and Edwards, David (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal, 11 (5). pp. 564-571. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12044)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

genomic instability

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)

genomics

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

genotyping by sequencing

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

haplotype

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

high-throughput sequencing

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

horticulture

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

host-plants

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

HTS

Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

Illumina

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

In vitro culture

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105. pp. 54-66. ISSN 0885-5765 (Print), 1096-1178 (Online) (doi:https://doi.org/10.1016/j.pmpp.2018.06.003)

Integration

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Ion Torrent

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

isothermal amplification

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: 0000-0002-3952-1562 , Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports, 14:12438. pp. 1-11. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-024-62249-y)

jasmonate

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

LAMP

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

leaf beetle

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

lineage specific

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

linkage map

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Maize streak virus

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

Markers

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

microsatellites

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

mitochondrial DNA

Kanyesigye, Dalton, Pius Alibu, Vincent, Tek Tay, Wee, Nalela, Polycarp, Paparu, Pamela, Olaboro, Samuel, Tamusange Nkalubo, Stanley, Siraj Kayondo, Ismail, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Seal, Susan ORCID: 0000-0002-3952-1562 and Hilary Otim, Michael (2022) Population genetic structure of the bean leaf beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. Insects, 13 (6):543. ISSN 2075-4450 (Online) (doi:https://doi.org/10.3390/insects13060543)

mitogenome

Khayi, Slimane ORCID: 0000-0001-8033-2117 , Armitage, Andrew ORCID: 0000-0002-0610-763X , El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: 0000-0003-1067-1652 , Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: 0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:https://doi.org/10.1080/23802359.2021.1978894)

Molecular biology

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

MSV

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: 0000-0002-0788-3243 , Chikoti, Patrick C., Seal, Susan ORCID: 0000-0002-3952-1562 and Silva, Gonҫalo ORCID: 0000-0001-5544-2947 (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports, 10:19633. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-020-76612-2)

multiplex PCR

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

mycology

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

next-generation sequencing

Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

Next-generation sequencing – SASSY – BAC – Assembly – 7DS – Triticum aestivum – Saccharum spp

Visendi, Paul, Berkman, Paul J., Hayashi, Satomi, Golicz, Agnieszka A., Bayer, Philipp E., Ruperao, Pradeep, Hurgobin, Bhavna, Montenegro, Juan, Chan, Chon-Kit Kenneth, Staňková, Helena, Batley, Jacqueline, Šimková, Hana, Doležel, Jaroslav and Edwards, David (2016) An efficient approach to BAC based assembly of complex genomes. Plant Methods, 12 (2). pp. 1-9. ISSN 1746-4811 (Print), 1746-4811 (Online) (doi:https://doi.org/10.1186/s13007-016-0107-9)

oomycete

Armitage, Andrew ORCID: 0000-0002-0610-763X , Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

Optical mapping

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

Oxford nanopore

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

Pacific biosciences

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

pandemic

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

pangenome

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

Pathogenic fungi

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Pathogenicity of plant pathogens

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Phoenix dactylifera

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

phylogenomics

Armitage, Andrew ORCID: 0000-0002-0610-763X , Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)

Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X , Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

Phylogeny

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Physical Map

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

phytopathology

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Tomlinson, Jenny, Onkokesung, Nawaporn, Sommer, Sarah, Mrisho, Latifa, Legg, James, Silva, Ian P., Gutierrez-Vazquez, Yaiza, Howard, Thomas P., Laverick, Alex, Hossain, Oindrila, Wei, Qingshan, M. Gold, Kaitlin and Boonham, Neil (2021) Plant pest surveillance: from satellites to molecules. Emerging Topics in Life Sciences, 5 (2). pp. 275-287. ISSN 2397-8554 (Print), 2397-8562 (Online) (doi:https://doi.org/10.1042/ETLS20200300)

Phytophthora

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

plant pathogen

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Plant pathology

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

plant virus

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

plant-pathogen

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: 0000-0002-0610-763X , Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)

polygenic

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Polyploidy

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

Potyvirus

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

primary metabolism

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

quantitative trait loci (QTLs)

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

rapid diagnosis

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: 0000-0002-3952-1562 , Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports, 14:12438. pp. 1-11. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-024-62249-y)

Recombination

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Reverse transcriptase recombinase polymerase amplification (RT-RPA)

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: 0000-0002-3952-1562 , Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports, 14:12438. pp. 1-11. ISSN 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-024-62249-y)

RNA-Seq

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105. pp. 54-66. ISSN 0885-5765 (Print), 1096-1178 (Online) (doi:https://doi.org/10.1016/j.pmpp.2018.06.003)

Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

Roche 454

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

Rolling circle amplification

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

RT-LAMP

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

Rubus

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

seed systems

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

Sequence diversity

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Sequencing

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

single nucleotide polymorphism (SNP)

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

single nucleotide polymorphisms

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation characterisation of cereal genomes for marker discovery. Biology, 2 (4). pp. 1357-1377. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology2041357)

Visendi, Paul, Batley, Jacqueline and Edwards, David (2013) Next generation sequencing and germplasm resources. Genomics of Plant Genetic Resources. Springer, Dordrecht, Holland, pp. 369-390. ISBN 978-9400775718 (doi:https://doi.org/10.1007/978-94-007-7572-5_15)

Small-spored Alternaria

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: 0000-0002-0610-763X , Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)

Sphaerotheca macularis

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: 0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)

SSA3

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

stress–signalling

Bömer, Moritz ORCID: 0000-0003-1003-9622 , O’Brien, José A., Pérez-Salamó, Imma, Krasauskas, Jovaras, Finch, Paul, Briones, Andrea, Daudi, Arsalan, Souda, Puneet, Tsui, Tjir-Li, Whitelegge, Julian P., Bolwell, G. Paul and Devoto, Alessandra (2018) COI1-dependent jasmonate signalling affects growth, metabolites production and cell wall protein composition in Arabidopsis. Annals of Botany, 122 (7). pp. 1117-1129. ISSN 0305-7364 (Print), 1095-8290 (Online) (doi:https://doi.org/10.1093/aob/mcy109)

Sub-Saharan Africa

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

surveillance

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Tomlinson, Jenny, Onkokesung, Nawaporn, Sommer, Sarah, Mrisho, Latifa, Legg, James, Silva, Ian P., Gutierrez-Vazquez, Yaiza, Howard, Thomas P., Laverick, Alex, Hossain, Oindrila, Wei, Qingshan, M. Gold, Kaitlin and Boonham, Neil (2021) Plant pest surveillance: from satellites to molecules. Emerging Topics in Life Sciences, 5 (2). pp. 275-287. ISSN 2397-8554 (Print), 2397-8562 (Online) (doi:https://doi.org/10.1042/ETLS20200300)

tebuconazole

Heaven, Thomas, Armitage, Andrew ORCID: 0000-0002-0610-763X , Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)

Thjileria Parva

Visendi, Paul, Ng'ang'a, Wanjiku, Bulimo, Wallace, Bishop, Richard, Ochanda, James and de Villiers, Etienne P. (2011) TparvaDB: a database to support Theileria parva vaccine development. Database, 2011. bar015-bar015. ISSN 1758-0463 (Online) (doi:https://doi.org/10.1093/database/bar015)

transposons

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)

Triticum aestivum

Berkman, Paul J., Visendi, Paul, Lee, Hong C., Stiller, Jiri, Manoli, Sahana, Lorenc, Michał T., Lai, Kaitao, Batley, Jacqueline, Fleury, Delphine, Šimková, Hana, Kubaláková, Marie, Weining, Song, Doležel, Jaroslav and Edwards, David (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal, 11 (5). pp. 564-571. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12044)

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

Tulpová, Zuzana, Luo, Ming-Cheng, Toegelová, Helena, Visendi, Paul, Hayashi, Satomi, Vojta, Petr, Paux, Etienne, Kilian, Andrzej, Abrouk, Michaël, Bartoš, Jan, Hajdúch, Marián, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology, 48. pp. 12-19. ISSN 1871-6784 (Print), 1876-4347 (Online) (doi:https://doi.org/10.1016/j.nbt.2018.03.003)

Uganda

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

vaccine development

Visendi, Paul, Ng'ang'a, Wanjiku, Bulimo, Wallace, Bishop, Richard, Ochanda, James and de Villiers, Etienne P. (2011) TparvaDB: a database to support Theileria parva vaccine development. Database, 2011. bar015-bar015. ISSN 1758-0463 (Online) (doi:https://doi.org/10.1093/database/bar015)

virus detection

Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

virus diagnostics

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

West Africa

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

wheat

Lorenc, Michał T., Hayashi, Satomi, Stiller, Jiri, Lee, Hong, Manoli, Sahana, Ruperao, Pradeep, Visendi, Paul, Berkman, Paul J., Lai, Kaitao, Batley, Jacqueline and Edwards, David (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology, 1 (3). pp. 370-382. ISSN 2079-7737 (Print), 2079-7737 (Online) (doi:https://doi.org/10.3390/biology1020370)

Montenegro, Juan D., Golicz, Agnieszka A., Bayer, Philipp E., Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Muhindira, Paul, Lai, Kaitao, Doležel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. The Plant Journal, 90 (5). pp. 1007-1013. ISSN 0960-7412 (doi:https://doi.org/10.1111/tpj.13515)

Staňková, Helena, Hastie, Alex R., Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav and Šimková, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 (7). pp. 1523-1531. ISSN 1467-7644 (Print), 1467-7652 (Online) (doi:https://doi.org/10.1111/pbi.12513)

whitefly species

Namuddu, Annet, Seal, Susan ORCID: 0000-0002-3952-1562 , van Brunschot, Sharon ORCID: 0000-0002-9634-9463 , Malka, Osnat, Kabaalu, Richard, Morin, Shai, Omongo, Christopher and Colvin, John (2023) Distribution of Bemisia tabaci in different agro-ecological regions in Uganda and the threat of vector-borne pandemics into new cassava growing areas. Frontiers in Sustainable Food Systems, 7:106810. pp. 1-15. ISSN 2571-581X (Online) (doi:https://doi.org/10.3389/fsufs.2023.1068109)

Yam

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: 0000-0001-5544-2947 and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-017-3605-9)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: 0000-0001-5544-2947 , Lava Kumar, P. and Seal, Susan ORCID: 0000-0002-3952-1562 (2018) Rolling circle amplification to screen yam germplasm for badnavirus infections and to amplify and characterise novel badnavirus genomes. Bio-protocol, 8 (1). ISSN 2331-8325 (Online) (doi:https://doi.org/10.21769/BioProtoc.2672)

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2016) A sequence-independent strategy for amplification and characterisation of episomal badnavirus sequences reveals three previously uncharacterised yam badnaviruses. Viruses, 8:188. pp. 1-22. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v8070188)

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

Silva, Goncalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2022) Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2022.846989)

Turaki, Aliyu A., Bömer, Moritz ORCID: 0000-0003-1003-9622 , Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2017) PCR-DGGE analysis: Unravelling complex mixtures of badnavirus sequences present in yam germplasm. Viruses, 9 (7). p. 181. ISSN 1999-4915 (Print), 1999-4915 (Online) (doi:https://doi.org/10.3390/v9070181)

Yam mosaic virus

Bömer, Moritz ORCID: 0000-0003-1003-9622 , Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology, 105. pp. 54-66. ISSN 0885-5765 (Print), 1096-1178 (Online) (doi:https://doi.org/10.1016/j.pmpp.2018.06.003)

Festus, Ruth, Seal, Susan ORCID: 0000-0002-3952-1562 , Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: 0000-0001-5544-2947 (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the rapid and sensitive detection of Yam mosaic virus. Viruses, 15 (7):1592. pp. 1-17. ISSN 1999-4915 (Online) (doi:https://doi.org/10.3390/v15071592)

YMV

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: 0000-0001-5544-2947 , Bömer, Moritz ORCID: 0000-0003-1003-9622 , Atiri, Gabriel I., Onyeka, Joseph, Maroya, Norbert G., Seal, Susan E. and Kumar, P. Lava (2018) Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Archives of Virology, 163 (4). pp. 1057-1061. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:https://doi.org/10.1007/s00705-018-3706-0)

This list was generated on Thu Jul 18 06:29:51 2024 UTC.