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