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高粱端粒到端粒基因组组装。

Telomere-to-telomere genome assembly of sorghum.

机构信息

Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.

BGI Genomics, Shenzhen, 518083, China.

出版信息

Sci Data. 2024 Aug 2;11(1):835. doi: 10.1038/s41597-024-03664-8.

DOI:10.1038/s41597-024-03664-8
PMID:39095379
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11297213/
Abstract

"Cuohu Bazi" (CHBZ) is an ancient sorghum variety collected from the fields of China, known for its agronomic traits like dwarf stature, early maturation. In this study, we present the first telomere-to-telomere (T2T) and gap-free genome assembly of CHBZ using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. The assembled genome comprises 724.85 Mb, effectively resolving all 3,913 gaps that were present in the previous sorghum BTx623 reference genome. Notably, the T2T assembly captures 10 centromeres and all 20 telomeres, providing strong support for their integrity. This assembly is of high quality in terms of contiguity (contig N50: 71.1 Mb), completeness (BUSCO score: 99.01%, k-mer completeness: 98.88%), and correctness (QV: 61.60). Repetitive sequences accounted for 70.41% of the genome and a total of 32,855 protein-coding genes have been annotated. Furthermore, 161 CHBZ-specific presence/absence variants genes have been identified when comparing to BTx623 genome. This study provides valuable insights for future research on sorghum genetics, genomics, and evolutionary history.

摘要

“挫花粑粑”（CHBZ）是一种古老的高粱品种，采集自中国田野，以其矮秆、早熟等农艺性状而闻名。在这项研究中，我们使用 PacBio HiFi 读取、Oxford Nanopore Technologies 和 Hi-C 数据首次完成了 CHBZ 的端粒到端粒（T2T）和无间隙基因组组装。组装的基因组包含 724.85 Mb，有效地解决了之前高粱 BTx623 参考基因组中存在的 3913 个缺口。值得注意的是，T2T 组装捕获了 10 个着丝粒和所有 20 个端粒，为其完整性提供了有力支持。该组装在连续性（contig N50：71.1 Mb）、完整性（BUSCO 得分：99.01%，k-mer 完整性：98.88%）和正确性（QV：61.60）方面具有很高的质量。重复序列占基因组的 70.41%，共注释了 32855 个蛋白质编码基因。此外，当与 BTx623 基因组比较时，鉴定出了 161 个 CHBZ 特异性的存在/缺失变异基因。本研究为高粱遗传、基因组学和进化历史的未来研究提供了有价值的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/16cbdbeb5149/41597_2024_3664_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/8e1fe181978b/41597_2024_3664_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/6c374428d576/41597_2024_3664_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/a67615cb3f94/41597_2024_3664_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/468f5d264e62/41597_2024_3664_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/16cbdbeb5149/41597_2024_3664_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/8e1fe181978b/41597_2024_3664_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/6c374428d576/41597_2024_3664_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/a67615cb3f94/41597_2024_3664_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/468f5d264e62/41597_2024_3664_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/85d6/11297213/16cbdbeb5149/41597_2024_3664_Fig5_HTML.jpg

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