The Plant Cell
Abstract
Centromeres are dynamic chromosomal regions and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza. We report a 12.4 Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ~15 Mya (million years ago). The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and ten in O. brachyantha. Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in Oryza brachyantha jumped ~ 400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P<2.2×10-16). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g. spreading or micro-repositioning) may drive such gene loss.
| 论文编号: | DOI:10.1105/tpc.18.00163 |
| 论文题目: | Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-driven Gene Escape from the Centromeric Regions |
| 英文论文题目: | Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-driven Gene Escape from the Centromeric Regions |
| 第一作者: | Yi Liao, Xuemei Zhang, Bo Li, Tieyan Liu, Jinfeng Chen, Zetao Bai, Meijiao Wang, Jinfeng Shi, Jason G. Walling, Rod A. Wing, Jiming Jiang, Mingsheng Chen |
| 英文第一作者: | Yi Liao, Xuemei Zhang, Bo Li, Tieyan Liu, Jinfeng Chen, Zetao Bai, Meijiao Wang, Jinfeng Shi, Jason G. Walling, Rod A. Wing, Jiming Jiang, Mingsheng Chen |
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| 发表年度: | 2018-07-04 |
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| 摘要: | Centromeres are dynamic chromosomal regions and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza. We report a 12.4 Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ~15 Mya (million years ago). The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and ten in O. brachyantha. Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in Oryza brachyantha jumped ~ 400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P<2.2×10-16). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g. spreading or micro-repositioning) may drive such gene loss. |
| 英文摘要: | Centromeres are dynamic chromosomal regions and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza. We report a 12.4 Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ~15 Mya (million years ago). The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and ten in O. brachyantha. Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in Oryza brachyantha jumped ~ 400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P<2.2×10-16). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g. spreading or micro-repositioning) may drive such gene loss. |
| 刊物名称: | The Plant Cell |
| 英文刊物名称: | The Plant Cell |
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| 其它备注: | Yi Liao, Xuemei Zhang, Bo Li, Tieyan Liu, Jinfeng Chen, Zetao Bai, Meijiao Wang, Jinfeng Shi, Jason G. Walling, Rod A. Wing, Jiming Jiang, Mingsheng Chen. Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-driven Gene Escape from the Centromeric Regions. The Plant Cell. DOI:10.1105/tpc.18.00163 |
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