Haplotype-resolved Assembly of a Pig Genome Using Single-sperm Sequencing

Overview

Journal Commun Biol

Specialty Biology

Date 2024 Jun 18

PMID 38890535

Authors

Yongchao Niu

Xinhao Fan

Yalan Yang

Jiang Li

Jinmin Lian

Liu Wang

Yongjin Zhang

Yijie Tang

Zhonglin Tang

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms.

Du H, Hu J, Zhang Z, Wu Z Animals (Basel). 2025; 15(4).

PMID: 40003085 PMC: 11851914. DOI: 10.3390/ani15040603.

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