中国农业大学李孟华等近期取得重要工作进展。他们通过研究绵羊端粒到端粒基因组组装识别出与羊毛细度相关的变异。相关研究成果2025年1月8日在线发表于《自然—遗传学》杂志上。

据介绍，目前为改进绵羊参考基因组组装所做的持续努力仍留下许多缺口和不完整区域，这导致基因组研究中出现一些常见的失误和错误。

研究人员报道了一只公羊的2.85Gb无间隙的端粒到端粒基因组（T2T-sheep1.0），其涵盖了所有常染色体以及X和Y染色体。该基因组在最新的参考组装版本ARS-UI_Ramb_v3.0基础上，新增了220.05Mb此前未解析的区域以及754个新基因；它在着丝粒区域包含四种重复单元（SatI、SatII、SatIII 和 CenY）。T2T-sheep1.0的碱基准确率超过99.999%，纠正了先前参考组装版本中的若干结构错误，并改进了重复序列中结构变异的检测。

研究人员将全球家养和野生绵羊的全基因组短读长序列与T2T-sheep1.0进行比对，在先前未解析的区域中鉴定出2664979个新的单核苷酸多态性，这改进了群体遗传学分析，以及对驯化（例如ABCC4基因）和羊毛细度（例如FOXQ1基因）选择信号的检测。

附：英文原文

Title: Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

Author: Luo, Ling-Yun, Wu, Hui, Zhao, Li-Ming, Zhang, Ya-Hui, Huang, Jia-Hui, Liu, Qiu-Yue, Wang, Hai-Tao, Mo, Dong-Xin, EEr, He-Hua, Zhang, Lian-Quan, Chen, Hai-Liang, Jia, Shan-Gang, Wang, Wei-Min, Li, Meng-Hua

Issue&Volume: 2025-01-08

Abstract: Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (T2T-sheep1.0), including all autosomes and the X and Y chromosomes. This genome adds 220.05Mb of previously unresolved regions and 754 new genes to the most updated reference assembly ARS-UI_Ramb_v3.0; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. T2T-sheep1.0 has a base accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against T2T-sheep1.0 identifies 2,664,979 new single-nucleotide polymorphisms in previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example, ABCC4) and wool fineness (for example, FOXQ1).

DOI: 10.1038/s41588-024-02037-6

Source: https://www.nature.com/articles/s41588-024-02037-6