中国粒用高粱654的端粒到端粒基因组组装

A telomere-to-telomere genome assembly of Chinese grain sorghum 654.

作者信息

Wang Fulin, Bao Jiandong, Zhang Heng, Zhai Guowei, Song Tao, Liu Zhijian, Han Yu, Yu Fan, Zou Guihua, Zhu Ying

机构信息

State Key Laboratory for Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.

State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.

出版信息

Sci Data. 2025 Mar 19;12(1):460. doi: 10.1038/s41597-025-04791-6.

DOI:10.1038/s41597-025-04791-6

PMID:40108243

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11923156/

Abstract

The grain sorghum inbred line 654 serves as a parent for numerous Chinese commercial hybrids and recombinant inbred lines (RILs), which have played a pivotal role in the cloning of several agronomically important traits. In this study, we present a telomere-to-telomere (T2T) genome assembly of the inbred line 654 (728.81 Mb) using PacBio HiFi, ultra-long Oxford Nanopore Technology, and Hi-C sequencing data. The T2T genome assembly has high integrity (contains all of 10 centromeres and 20 telomeres without any gaps), high contiguity (contig N90: 52.02 Mb), high completeness (98.33% BUSCO completeness, 98.88% k-mer completeness, and LAI 24.38), and extremely low base error (3.37 × 10, QV: 64.72). A total of 62.34% sequences were identified as repetitive, and rest region contained 44,399 protein-coding genes, of which 30,245 were functionally annotated. The gap-free T2T genome assembly enables the full picture of the potential translational genomics, and provides the highest resolution genetic map for future studies on genome evolution, structure variation, and the genetic control of agronomic traits in sorghum breeding.

摘要

高粱自交系654是众多中国商业杂交种和重组自交系（RIL）的亲本，这些杂交种和自交系在多个重要农艺性状的克隆中发挥了关键作用。在本研究中，我们利用PacBio HiFi、超长牛津纳米孔技术和Hi-C测序数据，对自交系654（728.81 Mb）进行了端粒到端粒（T2T）基因组组装。该T2T基因组组装具有高完整性（包含所有10个着丝粒和20个端粒，无任何缺口）、高连续性（contig N90：52.02 Mb）、高完整性（BUSCO完整性98.33%，k-mer完整性98.88%，LAI 24.38）和极低的碱基错误率（3.37×10，QV：64.72）。共鉴定出62.34%的序列为重复序列，其余区域包含44399个蛋白质编码基因，其中30245个具有功能注释。无缺口的T2T基因组组装能够全面了解潜在的翻译基因组学，并为高粱育种中未来的基因组进化、结构变异和农艺性状的遗传控制研究提供最高分辨率的遗传图谱。