# Haplotype-resolved assembly of the mule duck genome using high-fidelity sequencing technology

## TL;DR

This paper presents high-quality haplotype assemblies of a female mule duck genome, revealing structural variations and gene expression differences that could aid in duck breeding and functional genomics.

## Contribution

The study provides the first haplotype-resolved genome assembly of a mule duck with high continuity and completeness, along with insights into structural variations and haplotype-specific gene expression.

## Key findings

- The mule duck genome assemblies show high continuity and completeness, outperforming existing duck genomes.
- Structural variations correlate with autosome length, and haplotype-specific genes are involved in muscle-related biological processes.
- Haplotype-specific expression genes were identified, with similar biological functions in both haplotypes.

## Abstract

Mule duck is vitally important to the production of global duck meat. Here, we present two high-quality haplotypes of a female mule duck (haplotype 1 (H1):1.28 Gb, haplotype 2 (H2): 1.40 Gb). The continuity (H1: contig N50 = 14.90 Mb, H2: contig N50 = 15.70 Mb) and completeness (BUSCO: H1 = 96.9%, H2 = 97.3%) are substantially better than those of other duck genomes. We detected the structural variations (SVs) in H1 and H2. We observed a positive correlation between autosome length and the number of SVs. Z chromosome was some deficient in deletions and insertions, but W chromosome was some excessive. A total of 1,451 genes were haplotype specific expression (HSEs). Among them, 737 specifically expressed in H1, and 714 specifically expressed in H2. We found that H1 and H2 HSEs tended to be involved in similar biological processes, such as myometrial relaxation and contraction pathways, muscle structure development and phosphorylation. Our haplotype-resolved genome assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in mule duck.