Haplotype-resolved assembly of a pig genome using single-sperm sequencing

文献类型： 外文期刊

第一作者： Niu, Yongchao

作者： Niu, Yongchao;Fan, Xinhao;Yang, Yalan;Wang, Liu;Tang, Zhonglin;Niu, Yongchao;Fan, Xinhao;Yang, Yalan;Tang, Yijie;Tang, Zhonglin;Fan, Xinhao;Zhang, Yongjin;Tang, Zhonglin;Fan, Xinhao;Yang, Yalan;Tang, Yijie;Tang, Zhonglin;Li, Jiang;Lian, Jinmin

作者机构：

期刊名称：COMMUNICATIONS BIOLOGY （ 影响因子：5.2； 五年影响因子：5.6 ）

ISSN：

年卷期： 2024 年 7 卷 1 期

页码：

收录情况： SCI

摘要： Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motility trait to a specific region on chromosome 1 (105.40-110.70 Mb). Furthermore, with the assistance of Y chromosome-bearing sperm data, 26.16 Mb Y chromosome sequences were assembled. We report a reliable approach for assembling chromosome-level phased genomes and reveal the potential of sperm population in basic biology research and sperm phenotype research. An improved pig genome assembly is reported, using single sperm sequencing to reconstruct chromosome haplotypes, and with improved Y chromosome sequence.

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