Endogenous Pararetroviral Sequences (EPRVs) from Whole-Genome Sequencing of Five Dioscorea (Yam) Species

This dataset comprises endogenous pararetroviral sequences (EPRVs) mined from 86 publicly available whole-genome sequencing libraries across five yam species (Dioscorea rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). The primary focus is on the white yam (D. rotundata), which hosts a complex diversity of EPRVs that complicate pathogen diagnostics and germplasm exchange.
Sequences were identified using the CAULIFINDER pipeline, which targets the conserved Reverse Transcriptase/RNase H (RT/RNase H) domains of the Caulimoviridae family. Subsequent phylogenetic analyses revealed four major EPRV groups: Yendovirus, Badnavirus, Yam Endovirus 1, and a novel, previously uncharacterized Dioscovirus-like lineage.
A key feature of this dataset is the identification of both fragmented EPRV insertions and complete, full-length viral genomes within the Yam Badnavirus and Dioscovirus-like clades. These include sequences resembling linearized circular episomal viruses and integrated forms flanked by host genomic sequences.
Potential Applications:
Viral Diagnostics: Development of specific assays to differentiate harmful episomal viruses from endogenous EPRVs.Evolutionary Virology: Study of virus-host co-evolution, integration events, and potential reactivation mechanisms.Yam Breeding: Informing breeding programs by characterizing the "viral fossil record" within yam genomes to avoid unnecessary rejection of germplasm.Genome Surveillance: Serving as a reference for genome-wide surveillance in yam virology.Key Species: Dioscorea rotundata (White Yam), Dioscorea alata (Water Yam), Dioscorea praehensilis, Dioscorea abyssinica, Dioscorea dumetorum (Bitter Yam)