Badnavirus; Denaturing gradient gel electrophoresis (DGGE); Sequence diversity; Yam; Dioscorea spp.; Endogenous pararetrovirus (EPRV); Episomal badnavirus; Integration; Detection

Turaki, Aliyu A., Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Kumar, P. Lava and Seal, Susan E. ORCID: https://orcid.org/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:10.3390/v9070181)

Biotransformation; Phosphogypsum; Phylogenetic characterization; Sulfate-reducing bacteria

Martins, Mónica, Assunção, Ana, Neto, André, Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Sghaier, Haïtham and Costa, Maria Clara (2016) Performance and bacterial community shifts during phosphogypsum biotransformation. Water, Air, & Soil Pollution, 227 (12):437. pp. 1-10. ISSN 0049-6979 (Print), 1573-2932 (Online) (doi:10.1007/s11270-016-3129-z)

CTV, typing, CP phylogeny, stem-pitting, seedling yellows, quick decline, probe hybridisation

Nolasco, G., Santos, C., Silva, G. ORCID: https://orcid.org/0000-0001-5544-2947 and Fonseca, F. (2008) Development of an asymmetric PCR-ELISA typing method for citrus tristeza virus based on the coat protein gene. Journal of Virological Methods, 155 (2). pp. 97-108. ISSN 0166-0934 (doi:10.1016/j.jviromet.2008.09.030)

Citrus tristeza virus (CTV),

Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Marques, Natália and Nolasco, Gustavo (2011) The evolutionary rate of citrus tristeza virus ranks among the rates of the slowest RNA viruses. Journal of General Virology, 93 (2). pp. 419-429. ISSN 0022-1317 (Print), 1465-2099 (Online) (doi:10.1099/vir.0.036574-0)

Detection, GFLV, Vitis vinifera

Silva, G. ORCID: https://orcid.org/0000-0001-5544-2947, Lecourt, J., Clover, G.R.G. and Seal, S. E. ORCID: https://orcid.org/0000-0002-3952-1562 (2017) First report of Grapevine fanleaf virus infecting grapevine in the United Kingdom. New Disease Reports, 36 (9). ISSN 2044-0588 (Online) (doi:10.5197/j.2044-0588.2017.036.009)

Grapevine Pinot gris virus (GPGV)

Silva, G. ORCID: https://orcid.org/0000-0001-5544-2947, Lecourt, J., Clover, G.R.G. and Seal, S.E. ORCID: https://orcid.org/0000-0002-3952-1562 (2018) First record of Grapevine Pinot gris virus infecting Vitis vinifera in the United Kingdom. New Disease Reports, 38 (7). ISSN 2044-0588 (Online) (doi:10.5197/j.2044-0588.2018.038.007)

In vitro culture; RNA-Seq; Dioscorea spp.; Badnavirus; Yam mosaic virus

Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Rathnayake, Ajith I., Visendi, Paul, Sewe, Steven O., Sicat, Juan Paolo A., Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Kumar, P. Lava and Seal, Susan E. ORCID: https://orcid.org/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:10.1016/j.pmpp.2018.06.003)

MSV; Maize streak virus; diagnostics; LAMP; Food security; Capacity building

Tembo, Mathias, Adediji, Adedapo O., Bouvaine, Sophie ORCID: https://orcid.org/0000-0002-0788-3243, Chikoti, Patrick C., Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 and Silva, Gonҫalo ORCID: https://orcid.org/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:10.1038/s41598-020-76612-2)

RNA silencing suppressor, VSR, GFP, p21-like, Closterovirus

Marques, Natália T., Costa, Ângela A., Lopes, Débora, Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947 and Nolasco, Gustavo (2012) Comparing p20’s RNA silencing suppressing activity among five phylogenetic groups of Citrus Tristeza virus. European Journal of Plant Pathology, 133 (1). pp. 229-235. ISSN 0929-1873 (Print), 1573-8469 (Online) (doi:10.1007/s10658-011-9877-0)

RNA-Seq; virus detection; Betaflexiviridae; next-generation sequencing; HTS

Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Bömer, Moritz ORCID: https://orcid.org/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: https://orcid.org/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:10.3390/plants8060167)

Yam, Dioscorea spp., Episomal badnavirus, Endogenous pararetrovirus, DNA extraction, Diagnostics, Rolling circle amplification, Badna-PCR

Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Turaki, Aliyu, Rathnayake, Ajith, Silva, Goncalo ORCID: https://orcid.org/0000-0001-5544-2947, Lava Kumar, P. and Seal, Susan ORCID: https://orcid.org/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:10.21769/BioProtoc.2672)

Yam; Dioscorea spp.; Dioscorea rotundata; Episomal badnavirus; Endogenous Dioscorea bacilliform virus; Complete genome; Recombination; Phylogeny; West Africa

Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Rathnayake, Ajith I., Visendi, Paul, Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947 and Seal, Susan E. ORCID: https://orcid.org/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:10.1007/s00705-017-3605-9)

Yam; Recombinase polymerase amplification; Potyvirus; Isothermal amplification; Rapid diagnostics

Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Oyekanmi, Joshua, Nkere, Chukwuemeka K., Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Kumar, Lava P. and Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 (2018) Rapid detection of potyviruses from crude plant extracts. Analytical Biochemistry, 546. pp. 17-22. ISSN 0003-2697 (Print), 1096-0309 (Online) (doi:10.1016/j.ab.2018.01.019)

Yam; Dioscorea spp.; Virus; Ghana; Nigeria

Nkere, Chukwuemeka K., Otto, Emannuel, Atiri, Gabriel I., Onyeka, Joseph, Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 and Kumar, Lava P. (2020) Assessment of Yam mild mosaic virus coat protein gene sequence diversity reveals the prevalence of cosmopolitan and African group of isolates in Ghana and Nigeria. Current Plant Biology, 23:100156. ISSN 2214-6628 (Online) (doi:10.1016/j.cpb.2020.100156)

Yam; virus; diversity; diagnostic; impact; epidemiology; control

Diouf, Mame Boucar, Festus, Ruth, Silva, Goncalo ORCID: https://orcid.org/0000-0001-5544-2947, Guyader, Sébastien, Umber, Marie, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 and Teycheney, Pierre Yves (2022) Viruses of yams (Dioscorea spp.): current gaps in knowledge and future research directions to improve disease management. Viruses, 14 (9):1884. pp. 1-23. ISSN 1999-4915 (Online) (doi:10.3390/v14091884)

badnavirus; multiplex PCR; denaturing gradient gel electrophoresis (DGGE); endogenous badnaviral elements; yam; Dioscorea spp.; West Africa

Silva, Goncalo ORCID: https://orcid.org/0000-0001-5544-2947, Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Turaki, Aliyu A., Nkere, Chukwuemeka K., Kumar, P. Lava and Seal, Susan E. ORCID: https://orcid.org/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:10.3389/fpls.2022.846989)

biosecurity, diagnostics, phytopathology, surveillance

Silva, Goncalo ORCID: https://orcid.org/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:10.1042/ETLS20200300)

cassava brown streak viruses; early virus detection; isothermal amplification; rapid diagnosis; Reverse transcriptase recombinase polymerase amplification (RT-RPA)

Munguti, Florence M., Kilalo, Dora C., Yegon, Hillary K., Macharia, Isaac, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562, Mwango’mbe, Agnes W., Nyaboga, Evans N. and Silva, Goncalo ORCID: https://orcid.org/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:10.1038/s41598-024-62249-y)

closed‑tube reverse transcription loop‑mediated isothermal amplification (CT-RT-LAMP); YMV; Potyvirus; yam; Dioscorea; diagnostic assay

Nkere, Chukwuemeka K., Oyekanmi, Joshua O., Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Bömer, Moritz ORCID: https://orcid.org/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:10.1007/s00705-018-3706-0)

genetic differentiation; leaf beetle; mitochondrial DNA; microsatellites; haplotype; gene flow; 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: https://orcid.org/0000-0001-5544-2947, Seal, Susan ORCID: https://orcid.org/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:10.3390/insects13060543)

plant virus; high-throughput sequencing; bioinformatics; detection; discovery

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: https://orcid.org/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:10.3390/microorganisms9040841)

quality control; Illumina adapters; transcriptome assembly; Trimmomatic; trinity; Busco; Fastqc; Quast

Sewe, Steven, Silva, Goncalo ORCID: https://orcid.org/0000-0001-5544-2947, Sicat, Juan Paolo, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 and Muhindira, Paul Visendi (2022) Trimming and validation of Illumina short reads using Trimmomatic, trinity assembly, and assessment of RNA-Seq Data. In: Edwards, David, (ed.) Plant Bioinformatics. Methods in Molecular Biology. Springer Protocols, 2443 . Humana Press - Springer Nature, New York, United States, pp. 211-232. ISBN 978-1071620663 ; 978-1071620670 (doi:10.1007/978-1-0716-2067-0_11)

rice production, tabora, tanzania, village planning, rice cultivation, rice marketing, hydrology, water harnessing, water supply, draught animals, assessment mothodology

Silva, G.L. ORCID: https://orcid.org/0000-0001-5544-2947 (1989) Potential for improving rice production in Tabora Region, Tanzania and implications for village planning (ODNRI Bulletin No. 29). [Working Paper]

virology, medical microbiology, infectious diseases

Nolasco, G., Fonseca, F. and Silva, G. ORCID: https://orcid.org/0000-0001-5544-2947 (2007) Occurrence of genetic bottlenecks during citrus tristeza virus acquisition by Toxoptera citricida under field conditions. Archives of Virology, 153 (2). pp. 259-271. ISSN 0304-8608 (Print), 1432-8798 (Online) (doi:10.1007/s00705-007-1089-8)

yam, dioscorea spp., YMV, recombinase polymerase amplification, diagnosis

Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Nkere, Chukwuemeka, Kumar, P. Lava and Seal, Susan E. ORCID: https://orcid.org/0000-0002-3952-1562 (2015) Rapid and specific detection of Yam mosaic virus by reverse-transcription recombinase polymerase amplification. Journal of Virological Methods, 222. pp. 138-144. ISSN 0166-0934 (doi:10.1016/j.jviromet.2015.06.011)

yam; Dioscorea spp.; badnavirus; endogenous pararetrovirus; episomal badnavirus; diagnostics; rolling circle amplification; Sub-Saharan Africa

Bömer, Moritz ORCID: https://orcid.org/0000-0003-1003-9622, Turaki, Aliyu A., Silva, Gonçalo ORCID: https://orcid.org/0000-0001-5544-2947, Kumar, P. Lava and Seal, Susan E. ORCID: https://orcid.org/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:10.3390/v8070188)

yam; seed systems; Yam mosaic virus; virus diagnostics; isothermal amplification; RT-LAMP; West Africa

Festus, Ruth, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562, Prempeh, Ruth, Quain, Marian D. and Silva, Goncalo ORCID: https://orcid.org/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:10.3390/v15071592)