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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.

SUBMITTER: Chen J

PROVIDER: S-EPMC3615480 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

Chen Jinfeng J Huang Quanfei Q Gao Dongying D Wang Junyi J Lang Yongshan Y Liu Tieyan T Li Bo B Bai Zetao Z Luis Goicoechea Jose J Liang Chengzhi C Chen Chengbin C Zhang Wenli W Sun Shouhong S Liao Yi Y Zhang Xuemei X Yang Lu L Song Chengli C Wang Meijiao M Shi Jinfeng J Liu Geng G Liu Junjie J Zhou Heling H Zhou Weili W Yu Qiulin Q An Na N Chen Yan Y Cai Qingle Q Wang Bo B Liu Binghang B Min Jiumeng J Huang Ying Y Wu Honglong H Li Zhenyu Z Zhang Yong Y Yin Ye Y Song Wenqin W Jiang Jiming J Jackson Scott A SA Wing Rod A RA Wang Jun J Chen Mingsheng M

Nature communications 20130101

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 po ...[more]

PMID: 23481403

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Project description:Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels and CNV.

Dataset Information

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

Publications

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

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