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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Abstract	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.
AbstractList	IntroductionRice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. 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 Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon.MethodsThe eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (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.Results and discussionTen 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. Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. 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 Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon.IntroductionRice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. 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 Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon.The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (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.MethodsThe eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (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.Results and discussionTen 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. 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.
Author	Koide, Yohei Zhou, Zhitong Chen, Sunlu Encabo, Jaymee R. Koyanagi, Kanako O. Saito, Nozomi Kishima, Yuji Choi, Il-Ryong Kitajima, Katsuya Diaz, Maria Genaleen Q.
AuthorAffiliation	1 Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan 3 Graduate School of Information Science and Technology, Hokkaido University , Sapporo, Hokkaido , Japan 4 Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines , Los Baños, Laguna , Philippines 5 Rice Breeding Platform, International Rice Research Institute , Los Baños, Laguna , Philippines 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University , Nanjing , China 6 Faculty of Information Science and Technology, Hokkaido University , Sapporo, Hokkaido , Japan
AuthorAffiliation_xml	– name: 6 Faculty of Information Science and Technology, Hokkaido University , Sapporo, Hokkaido , Japan – name: 1 Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan – name: 4 Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines , Los Baños, Laguna , Philippines – name: 3 Graduate School of Information Science and Technology, Hokkaido University , Sapporo, Hokkaido , Japan – name: 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University , Nanjing , China – name: 5 Rice Breeding Platform, International Rice Research Institute , Los Baños, Laguna , Philippines
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Keywords	local chromosomal evolution Oryza AA-genome species phylogenetic incongruence introgression rearrangement eRTBVL-D
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Snippet	Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family . These viral elements, known... IntroductionRice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae .... Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral... IntroductionRice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae....
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SubjectTerms	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
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Title	Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species
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