Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China.
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Commun Biol. 2024 Jun 18;7(1):738. doi: 10.1038/s42003-024-06397-x.
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.
单细胞测序与长读长测序相结合，可以可靠地产生染色体水平的相基因组。在这项研究中，我们对一头雄性长白猪进行了 PacBio HiFi 和 Hi-C 测序，并对其 102 个精子细胞进行了单细胞测序。我们开发了一种基于长读长测序和精子相标记的单倍型组装方法。染色体水平的相组装比仅依赖 HiFi 读数的方法具有更高的相精度。使用单细胞测序数据成功构建了遗传图谱，将精子运动性状成功定位到 1 号染色体上的一个特定区域（105.40-110.70 Mb）。此外，借助携带 Y 染色体的精子数据，组装了 26.16 Mb 的 Y 染色体序列。我们报告了一种可靠的方法来组装染色体水平的相基因组，并揭示了精子群体在基础生物学研究和精子表型研究中的潜力。
