淮猪（Sus scrofa）的染色体水平基因组组装

Chromosome-level genome assembly of Huai pig (Sus scrofa).

作者信息

Du Heng, Lu Shiyu, Huang Qianqian, Zhou Lei, Liu Jian-Feng

机构信息

State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China.

出版信息

Sci Data. 2024 Oct 2;11(1):1072. doi: 10.1038/s41597-024-03921-w.

DOI:10.1038/s41597-024-03921-w

PMID:39358406

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11446922/

Abstract

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs.

摘要

尽管长读长测序技术和基因组组装技术的进步推动了基因组研究，但对于包括淮猪在内的中国独特本土猪种的基因组却知之甚少。淮猪是一种古老的家猪品种，与欧洲家猪相比，其肉色更红且对饲料的耐受性更高，这一点有充分的文献记载。在本研究中，我们使用PacBio、Hi-C和Illumina测序技术对淮猪基因组进行了测序和组装。最终得到的高度连续的染色体水平的淮猪基因组跨度为2.53 Gb，支架N50为138.92 Mb。组装基因组的基准通用单拷贝直系同源基因（BUSCO）完整性评分为95.33%。值得注意的是，淮猪基因组中注释了23,389个蛋白质编码基因，以及45.87%的重复序列。总体而言，本研究为未来中国家猪的遗传研究提供了新的基础资源。