AUTHOR=Saito Nozomi , Chen Sunlu , Kitajima Katsuya , Zhou Zhitong , Koide Yohei , Encabo Jaymee R. , Diaz Maria Genaleen Q. , Choi Il-Ryong , Koyanagi Kanako O. , Kishima Yuji 

TITLE=Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1261705

DOI=10.3389/fpls.2023.1261705

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family <italic>Caulimoviridae</italic>. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice <italic>Oryza sativa</italic> (spp. <italic>japonica</italic> and <italic>indica</italic>) and the closely related wild species <italic>Oryza rufipogon</italic>.</p></sec><sec><title>Methods</title><p>The eRTBVL-D sequences are widely distributed within these and other <italic>Oryza</italic> AA-genome species. Fifteen eRTBVL-D segments identified in the <italic>japonica</italic> (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species.</p></sec><sec><title>Results and discussion</title><p>Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region–specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.</p></sec>