title: Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
abstract: The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Chen
authors.forename: Quanfei
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authors.lastname: Huang
authors.forename: Dongying
authors.initials: D
authors.lastname: Gao
authors.forename: Junyi
authors.initials: J
authors.lastname: Wang
authors.forename: Yongshan
authors.initials: Y
authors.lastname: Lang
authors.forename: Tieyan
authors.initials: T
authors.lastname: Liu
authors.forename: Bo
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authors.lastname: Li
authors.forename: Zetao
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authors.lastname: Bai
authors.forename: Jose
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authors.lastname: Luis Goicoechea
authors.forename: Chengzhi
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authors.lastname: Liang
authors.forename: Chengbin
authors.initials: C
authors.lastname: Chen
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.forename: Shouhong
authors.initials: S
authors.lastname: Sun
authors.forename: Yi
authors.initials: Y
authors.lastname: Liao
authors.forename: Xuemei
authors.initials: X
authors.lastname: Zhang
authors.forename: Lu
authors.initials: L
authors.lastname: Yang
authors.forename: Chengli
authors.initials: C
authors.lastname: Song
authors.forename: Meijiao
authors.initials: M
authors.lastname: Wang
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Shi
authors.forename: Geng
authors.initials: G
authors.lastname: Liu
authors.forename: Junjie
authors.initials: J
authors.lastname: Liu
authors.forename: Heling
authors.initials: H
authors.lastname: Zhou
authors.forename: Weili
authors.initials: W
authors.lastname: Zhou
authors.forename: Qiulin
authors.initials: Q
authors.lastname: Yu
authors.forename: Na
authors.initials: N
authors.lastname: An
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.forename: Qingle
authors.initials: Q
authors.lastname: Cai
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Binghang
authors.initials: B
authors.lastname: Liu
authors.forename: Jiumeng
authors.initials: J
authors.lastname: Min
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
authors.forename: Honglong
authors.initials: H
authors.lastname: Wu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Ye
authors.initials: Y
authors.lastname: Yin
authors.forename: Wenqin
authors.initials: W
authors.lastname: Song
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D059646:Genome Size / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D016254:Mutagenesis, Insertional / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D056916:Segmental Duplications, Genomic / Q000235:genetics; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D002843:Chromatin; D018626:Retroelements