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

Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family . 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 p...

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Vydáno v:Frontiers in plant science Ročník 14; s. 1261705
Hlavní autoři: 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
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland Frontiers Media SA 27.10.2023
Frontiers Media S.A
Témata:
Chromosomes
Cultivation
eRTBVL-D
Evolution
Flowers & plants
Genetic diversity
Genomes
Grain cultivation
Interspecific hybridization
Introduced species
introgression
local chromosomal evolution
Oryza
Oryza AA-genome species
phylogenetic incongruence
Phylogenetics
Phylogeny
Plant Science
rearrangement
Rice
Segments
Speciation
Species diversity
Topology
Tungro
Viruses
local chromosomal evolution
Oryza AA-genome species
phylogenetic incongruence
introgression
rearrangement
eRTBVL-D
ISSN:1664-462X, 1664-462X
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Shrnutí:Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family . 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 (spp. and ) and the closely related wild species . The eRTBVL-D sequences are widely distributed within these and other AA-genome species. Fifteen eRTBVL-D segments identified in the (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. 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.
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Edited by: Nikolai Borisjuk, Huaiyin Normal University, China
Reviewed by: Xun Chen, Kyoto University, Japan; Mei-Yeh Jade Lu, Academia Sinica, Taiwan
ISSN:1664-462X
1664-462X
DOI:10.3389/fpls.2023.1261705