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Characterization of endogenous pararetroviruses in yam (Dioscorea spp.) genomes revealed four pararetrovirus groups, including a dioscovirus-like lineage: implications for diagnostics and yam germplasm exchange.

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Τίτλος: Characterization of endogenous pararetroviruses in yam (Dioscorea spp.) genomes revealed four pararetrovirus groups, including a dioscovirus-like lineage: implications for diagnostics and yam germplasm exchange.
Συγγραφείς: Osundahunsi BO; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria. bolajiosundahunsi@gmail.com., Moshood L; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria., Kolade OA; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria., Odu BO; Department of Crop Production and Protection, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria., Lava Kumar P; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria. L.Kumar@cgiar.org.
Πηγή: Archives of virology [Arch Virol] 2026 Aug 07; Vol. 171 (9). Date of Electronic Publication: 2026 Aug 07.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Springer-Verlag Country of Publication: Austria NLM ID: 7506870 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-8798 (Electronic) Linking ISSN: 03048608 NLM ISO Abbreviation: Arch Virol Subsets: MEDLINE
Imprint Name(s): Original Publication: Wien, New York, Springer-Verlag.
Ιατρικοί όροι (MeSH): Dioscorea*/virology , Dioscorea*/genetics , Plant Diseases*/virology , Caulimoviridae*/genetics , Caulimoviridae*/classification , Caulimoviridae*/isolation & purification , Genome, Viral*, Badnavirus/genetics ; Phylogeny ; Genome, Plant ; Genetic Variation
Περίληψη: Yams (Dioscorea spp.) are an important vegetatively propagated food security crop grown for their starchy tubers. Yams are susceptible to several viruses, and their genomes harbor a diverse array of endogenous pararetroviral sequences (EPRVs), which complicate diagnostics and germplasm exchange because of their similarity to episomal viruses. To better characterize EPRV diversity, we analyzed 86 publicly available whole-genome sequences from five Dioscorea species (D. rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). Assembled genomes were screened for endogenous pararetrovirus sequences (EPRVs) using the CAULIFINDER pipeline, targeting conserved RT/RNase H domains of the Caulimoviridae family. Our analyses revealed four major EPRV groups in D. rotundata: Yendovirus, Badnavirus, Yam Endovirus 1, and a Dioscovirus-like lineage. While most insertions were fragmented, we found full-length putative viral genomes corresponding to the Yam Badnavirus and Dioscovirus-like clades. These findings expand knowledge of yam EPRV diversity, contribute to the development of improved diagnostic tools to differentiate endogenous and episomal forms, and promote a science-based, risk-proportionate approach to yam phytosanitation that facilitates global germplasm exchange while maintaining biosecurity.
(© 2026. The Author(s).)
Competing Interests: Declarations. Competing interests: The authors declare that there are no conflicts of interest.
References: Arch Virol. 2018 Feb;163(2):533-538. (PMID: 29134336)
Mol Plant Pathol. 2014 Oct;15(8):790-801. (PMID: 24605894)
Arch Virol. 2017 Feb;162(2):517-521. (PMID: 27770216)
Proc Natl Acad Sci U S A. 2020 Dec 15;117(50):31987-31992. (PMID: 33268496)
Viruses. 2022 Aug 26;14(9):. (PMID: 36146691)
PLoS One. 2018 Sep 12;13(9):e0203038. (PMID: 30208072)
Curr Opin Virol. 2013 Dec;3(6):615-20. (PMID: 24035682)
Nat Commun. 2014 Nov 10;5:5269. (PMID: 25381880)
PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: 22039361)
Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700)
Brief Bioinform. 2019 Jul 19;20(4):1160-1166. (PMID: 28968734)
Nat Methods. 2017 Jun;14(6):587-589. (PMID: 28481363)
Arch Virol. 2007;152(4):819-25. (PMID: 17195956)
Bioinformatics. 2012 Dec 1;28(23):3150-2. (PMID: 23060610)
Arch Virol. 2003 Oct;148(10):1957-68. (PMID: 14551818)
Mol Biol Evol. 2023 Jan 4;40(1):. (PMID: 36322467)
BMC Plant Biol. 2007 May 21;7:24. (PMID: 17517142)
Bioinformatics. 2016 Apr 1;32(7):1009-15. (PMID: 26589280)
Arch Virol. 2008;153(5):877-89. (PMID: 18330495)
Mob DNA. 2022 Dec 3;13(1):31. (PMID: 36463202)
Virology. 2024 Mar;591:109991. (PMID: 38242059)
J Virol. 2008 Jul;82(13):6697-710. (PMID: 18417582)
Arch Virol. 2008;153(12):2263-72. (PMID: 19030955)
Virus Res. 2014 Jun 24;186:144-54. (PMID: 24457074)
Front Plant Sci. 2022 Dec 14;13:1011565. (PMID: 36589050)
Sci Rep. 2018 Jan 12;8(1):572. (PMID: 29330451)
PLoS Pathog. 2017 Jun 29;13(6):e1006413. (PMID: 28662199)
J Gen Virol. 2020 Oct;101(10):1025-1026. (PMID: 32940596)
Arch Virol. 2009;154(2):297-314. (PMID: 19190853)
Mol Plant Pathol. 2021 Feb;22(2):216-230. (PMID: 33231927)
J Virol. 2013 Aug;87(15):8624-37. (PMID: 23720724)
BMC Biol. 2017 Sep 19;15(1):86. (PMID: 28927400)
Arch Virol. 2010;155(1):123-31. (PMID: 19898772)
Virus Res. 2014 Jun 24;186:155-62. (PMID: 24457073)
Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405. (PMID: 27956617)
Grant Information: CGIARs Trust Fund donors Genebanks, Plant Health Initiative, and Sustainable Farming Program
Entry Date(s): Date Created: 20260807 Date Completed: 20260807 Latest Revision: 20260923
Update Code: 20260923
PubMed Central ID: PMC13451355
DOI: 10.1007/s00705-026-06703-4
PMID: 42566103
Βάση Δεδομένων: MEDLINE
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  Data: Characterization of endogenous pararetroviruses in yam (Dioscorea spp.) genomes revealed four pararetrovirus groups, including a dioscovirus-like lineage: implications for diagnostics and yam germplasm exchange.
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  Data: <searchLink fieldCode="AU" term="%22Osundahunsi+BO%22">Osundahunsi BO</searchLink>; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria. bolajiosundahunsi@gmail.com.<br /><searchLink fieldCode="AU" term="%22Moshood+L%22">Moshood L</searchLink>; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria.<br /><searchLink fieldCode="AU" term="%22Kolade+OA%22">Kolade OA</searchLink>; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria.<br /><searchLink fieldCode="AU" term="%22Odu+BO%22">Odu BO</searchLink>; Department of Crop Production and Protection, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria.<br /><searchLink fieldCode="AU" term="%22Lava+Kumar+P%22">Lava Kumar P</searchLink>; International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria. L.Kumar@cgiar.org.
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  Data: <searchLink fieldCode="JN" term="%227506870%22">Archives of virology</searchLink> [Arch Virol] 2026 Aug 07; Vol. 171 (9). <i>Date of Electronic Publication: </i>2026 Aug 07.
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– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Yams (Dioscorea spp.) are an important vegetatively propagated food security crop grown for their starchy tubers. Yams are susceptible to several viruses, and their genomes harbor a diverse array of endogenous pararetroviral sequences (EPRVs), which complicate diagnostics and germplasm exchange because of their similarity to episomal viruses. To better characterize EPRV diversity, we analyzed 86 publicly available whole-genome sequences from five Dioscorea species (D. rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). Assembled genomes were screened for endogenous pararetrovirus sequences (EPRVs) using the CAULIFINDER pipeline, targeting conserved RT/RNase H domains of the Caulimoviridae family. Our analyses revealed four major EPRV groups in D. rotundata: Yendovirus, Badnavirus, Yam Endovirus 1, and a Dioscovirus-like lineage. While most insertions were fragmented, we found full-length putative viral genomes corresponding to the Yam Badnavirus and Dioscovirus-like clades. These findings expand knowledge of yam EPRV diversity, contribute to the development of improved diagnostic tools to differentiate endogenous and episomal forms, and promote a science-based, risk-proportionate approach to yam phytosanitation that facilitates global germplasm exchange while maintaining biosecurity.<br /> (© 2026. The Author(s).)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: Declarations. Competing interests: The authors declare that there are no conflicts of interest.
– Name: Ref
  Label: References
  Group: RefInfo
  Data: Arch Virol. 2018 Feb;163(2):533-538. (PMID: <searchLink fieldCode="PM" term="%2229134336%22">29134336)</searchLink><br />Mol Plant Pathol. 2014 Oct;15(8):790-801. (PMID: <searchLink fieldCode="PM" term="%2224605894%22">24605894)</searchLink><br />Arch Virol. 2017 Feb;162(2):517-521. (PMID: <searchLink fieldCode="PM" term="%2227770216%22">27770216)</searchLink><br />Proc Natl Acad Sci U S A. 2020 Dec 15;117(50):31987-31992. (PMID: <searchLink fieldCode="PM" term="%2233268496%22">33268496)</searchLink><br />Viruses. 2022 Aug 26;14(9):. (PMID: <searchLink fieldCode="PM" term="%2236146691%22">36146691)</searchLink><br />PLoS One. 2018 Sep 12;13(9):e0203038. (PMID: <searchLink fieldCode="PM" term="%2230208072%22">30208072)</searchLink><br />Curr Opin Virol. 2013 Dec;3(6):615-20. (PMID: <searchLink fieldCode="PM" term="%2224035682%22">24035682)</searchLink><br />Nat Commun. 2014 Nov 10;5:5269. (PMID: <searchLink fieldCode="PM" term="%2225381880%22">25381880)</searchLink><br />PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: <searchLink fieldCode="PM" term="%2222039361%22">22039361)</searchLink><br />Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: <searchLink fieldCode="PM" term="%2232011700%22">32011700)</searchLink><br />Brief Bioinform. 2019 Jul 19;20(4):1160-1166. (PMID: <searchLink fieldCode="PM" term="%2228968734%22">28968734)</searchLink><br />Nat Methods. 2017 Jun;14(6):587-589. (PMID: <searchLink fieldCode="PM" term="%2228481363%22">28481363)</searchLink><br />Arch Virol. 2007;152(4):819-25. (PMID: <searchLink fieldCode="PM" term="%2217195956%22">17195956)</searchLink><br />Bioinformatics. 2012 Dec 1;28(23):3150-2. (PMID: <searchLink fieldCode="PM" term="%2223060610%22">23060610)</searchLink><br />Arch Virol. 2003 Oct;148(10):1957-68. (PMID: <searchLink fieldCode="PM" term="%2214551818%22">14551818)</searchLink><br />Mol Biol Evol. 2023 Jan 4;40(1):. (PMID: <searchLink fieldCode="PM" term="%2236322467%22">36322467)</searchLink><br />BMC Plant Biol. 2007 May 21;7:24. (PMID: <searchLink fieldCode="PM" term="%2217517142%22">17517142)</searchLink><br />Bioinformatics. 2016 Apr 1;32(7):1009-15. (PMID: <searchLink fieldCode="PM" term="%2226589280%22">26589280)</searchLink><br />Arch Virol. 2008;153(5):877-89. (PMID: <searchLink fieldCode="PM" term="%2218330495%22">18330495)</searchLink><br />Mob DNA. 2022 Dec 3;13(1):31. (PMID: <searchLink fieldCode="PM" term="%2236463202%22">36463202)</searchLink><br />Virology. 2024 Mar;591:109991. (PMID: <searchLink fieldCode="PM" term="%2238242059%22">38242059)</searchLink><br />J Virol. 2008 Jul;82(13):6697-710. (PMID: <searchLink fieldCode="PM" term="%2218417582%22">18417582)</searchLink><br />Arch Virol. 2008;153(12):2263-72. (PMID: <searchLink fieldCode="PM" term="%2219030955%22">19030955)</searchLink><br />Virus Res. 2014 Jun 24;186:144-54. (PMID: <searchLink fieldCode="PM" term="%2224457074%22">24457074)</searchLink><br />Front Plant Sci. 2022 Dec 14;13:1011565. (PMID: <searchLink fieldCode="PM" term="%2236589050%22">36589050)</searchLink><br />Sci Rep. 2018 Jan 12;8(1):572. (PMID: <searchLink fieldCode="PM" term="%2229330451%22">29330451)</searchLink><br />PLoS Pathog. 2017 Jun 29;13(6):e1006413. (PMID: <searchLink fieldCode="PM" term="%2228662199%22">28662199)</searchLink><br />J Gen Virol. 2020 Oct;101(10):1025-1026. (PMID: <searchLink fieldCode="PM" term="%2232940596%22">32940596)</searchLink><br />Arch Virol. 2009;154(2):297-314. (PMID: <searchLink fieldCode="PM" term="%2219190853%22">19190853)</searchLink><br />Mol Plant Pathol. 2021 Feb;22(2):216-230. (PMID: <searchLink fieldCode="PM" term="%2233231927%22">33231927)</searchLink><br />J Virol. 2013 Aug;87(15):8624-37. (PMID: <searchLink fieldCode="PM" term="%2223720724%22">23720724)</searchLink><br />BMC Biol. 2017 Sep 19;15(1):86. (PMID: <searchLink fieldCode="PM" term="%2228927400%22">28927400)</searchLink><br />Arch Virol. 2010;155(1):123-31. (PMID: <searchLink fieldCode="PM" term="%2219898772%22">19898772)</searchLink><br />Virus Res. 2014 Jun 24;186:155-62. (PMID: <searchLink fieldCode="PM" term="%2224457073%22">24457073)</searchLink><br />Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405. (PMID: <searchLink fieldCode="PM" term="%2227956617%22">27956617)</searchLink>
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  Data: CGIARs Trust Fund donors Genebanks, Plant Health Initiative, and Sustainable Farming Program
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      – TitleFull: Characterization of endogenous pararetroviruses in yam (Dioscorea spp.) genomes revealed four pararetrovirus groups, including a dioscovirus-like lineage: implications for diagnostics and yam germplasm exchange.
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