title: Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation.
abstract: Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.
authors.affiliation: Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Sunlu
authors.initials: S
authors.lastname: Chen
authors.affiliation: Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Ruifang
authors.initials: R
authors.lastname: Liu
authors.affiliation: Laboratory of Genome Sciences, Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
authors.forename: Kanako O
authors.initials: KO
authors.lastname: Koyanagi
authors.affiliation: Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan. Electronic address: kishima@abs.agr.hokuda.ac.jp.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kishima
mesh_terms: D052639:Caulimoviridae / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D049810:Genetic Speciation; D018745:Genome, Plant / Q000235:genetics*; D015613:Hepadnaviridae / Q000145:classification / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000821:virology; D010802:Phylogeny; D010942:Plant Viruses / Q000145:classification / Q000235:genetics*
keywords: Endogenous pararetrovirus; Genealogy; Paleovirology; Recombination; Rice; Rice speciation; Rice tungro bacilliform virus; Virus lineage