Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome.

IF 3.5 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2024-10-14 DOI:10.1186/s12864-024-10843-9

Yun Xia, Douyue Li, Tingyi Chen, Saichao Pan, Hanrou Huang, Wenxiang Zhang, Yulin Liang, Yongzhuo Fu, Zhuli Peng, Hongxi Zhang, Liang Zhang, Shan Peng, Ruixue Shi, Xingxin He, Siqian Zhou, Weili Jiao, Xiangyan Zhao, Xiaolong Wu, Lan Zhou, Jingyu Zhou, Qingjian Ouyang, You Tian, Xiaoping Jiang, Yi Zhou, Shiying Tang, Junxiong Shen, Kazusato Ohshima, Zhongyang Tan

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Abstract

Background: Microsatellites are increasingly realized to have biological significance in human genome and health in past decades, the assembled complete reference sequence of human genome T2T-CHM13 brought great help for a comprehensive study of short tandem repeats in the human genome.

Results: Microsatellites density landscapes of all 24 chromosomes were built here for the first complete reference sequence of human genome T2T-CHM13. These landscapes showed that short tandem repeats (STRs) are prone to aggregate characteristically to form a large number of STRs density peaks. We classified 8,823 High Microsatellites Density Peaks (HMDPs), 35,257 Middle Microsatellites Density Peaks (MMDPs) and 199, 649 Low Microsatellites Density Peaks (LMDPs) on the 24 chromosomes; and also classified the motif types of every microsatellites density peak. These STRs density aggregation peaks are mainly composing of a single motif, and AT is the most dominant motif, followed by AATGG and CCATT motifs. And 514 genomic regions were characterized by microsatellite density feature in the full T2T-CHM13 genome.

Conclusions: These landscape maps exhibited that microsatellites aggregate in many genomic positions to form a large number of microsatellite density peaks with composing of mainly single motif type in the complete reference genome, indicating that the local microsatellites density varies enormously along the every chromosome of T2T-CHM13.

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微卫星密度图显示了完整参考人类基因组中短串联重复序列的聚集情况。

背景：过去几十年来，人们越来越认识到微卫星在人类基因组和健康中的生物学意义，人类基因组T2T-CHM13完整参考序列的组装为全面研究人类基因组中的短串联重复序列提供了巨大帮助：结果：在人类基因组T2T-CHM13的第一个完整参考序列中，建立了全部24条染色体的微卫星密度图谱。这些图谱显示，短串联重复序列（STR）容易聚集形成大量的STR密度峰。我们对 24 条染色体上的 8823 个高微卫星密度峰（HMDP）、35257 个中微卫星密度峰（MMDP）和 199649 个低微卫星密度峰（LMDP）进行了分类，并对每个微卫星密度峰的主题类型进行了分类。这些 STRs 密度聚集峰主要由单一图案构成，其中 AT 是最主要的图案，其次是 AATGG 和 CCATT 图案。T2T-CHM13全基因组中有514个基因组区域具有微卫星密度特征：这些图谱显示，在完整的参考基因组中，微卫星在许多基因组位置聚集，形成了大量的微卫星密度峰，且主要由单一的图案类型组成，这表明在T2T-CHM13的每条染色体上，局部微卫星的密度差异巨大。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.