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

## TL;DR

This study creates a high-quality genome assembly for the Meishan pig and identifies genes linked to its domestication and high fertility.

## Contribution

The study provides a chromosome-level Meishan pig genome and identifies domestication-related genes using comparative genomics.

## Key findings

- A high-quality Meishan pig genome (MSjxau) was assembled with 96.2% completeness and 2.45 Gb size.
- 716 selective sweep intervals were identified, including the PGR gene linked to high fertility in Meishan pigs.
- The study contributes a structural variants resource by combining the new genome with 28 publicly available pig genomes.

## Abstract

This study assembled a high-quality chromosome-level genome of the Meishan pig using Illumina and PacBio sequencing technologies. By integrating this new genome with existing pig genome assemblies, we contribute to developing a pig pan-genome, facilitating research on structural variations. Selective sweep analysis between the Chinese wild boar and the Meishan pig revealed key candidate genes, such as TBX19 and PGR, linked to domestication traits. These findings provide valuable genetic resources for studying Meishan pig biology and offer a foundation for improving breeding strategies and conservation efforts.

Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene PGR may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs.