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高质量的长粒野稻染色体水平基因组。

A high-quality chromosome-level wild rice genome of Oryza coarctata.

机构信息

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium.

出版信息

Sci Data. 2023 Oct 14;10(1):701. doi: 10.1038/s41597-023-02594-1.

DOI:10.1038/s41597-023-02594-1
PMID:37838726
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10576809/
Abstract

Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.

摘要

籼稻野败（2n=4X=48，KKLL）是一种异源四倍体、未驯化的水稻近缘种，是唯一一种具有耐盐和耐淹特性的稻属物种。因此，它含有对水稻很重要的胁迫和耐受基因/因子。最初发表的基因组草图受到数据和技术限制的限制，导致组装结果不完整且高度碎片化。本研究报告了籼稻野败的一个新的、高度连续的染色体水平的基因组组装和注释。PacBio 高质量 HiFi reads 生成了 460 个总长度为 573.4 Mb 的 contigs，N50 为 23.1 Mb，这些 contigs 与 Hi-C 数据组装成 scaffolds，将 96.99%的组装结果锚定在 24 条染色体上。基因组组装包含 45571 个基因，重复序列占基因组的 25.5%。本研究首次鉴定了稻属的 KK 和 LL 基因组类型，为水稻基因组进化提供了有价值的见解。籼稻野败的染色体水平基因组组装为水稻研究和分子育种提供了有价值的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/e3fed04ffcbb/41597_2023_2594_Fig10_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/b19bad0211cf/41597_2023_2594_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/e3fed04ffcbb/41597_2023_2594_Fig10_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/d29cb6ae2e8e/41597_2023_2594_Fig2_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/fff11ea37eb4/41597_2023_2594_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/8bdef755ae86/41597_2023_2594_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/b9019144a2eb/41597_2023_2594_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/3a53c54ba48d/41597_2023_2594_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/b19bad0211cf/41597_2023_2594_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a4c1/10576809/e3fed04ffcbb/41597_2023_2594_Fig10_HTML.jpg

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