A telomere-to-telomere genome assembly of the Kaijiang duck and a reference-guided pangenome graph resource for duck genomes

This dataset integrates ONT, HiFi, Hi-C, and NGS sequencing technologies to generate a high-contiguity, T2T-level female duck reference genome and a chromosomal-level reference genome for the Kaijiang male duck, a geographical indication product of Dazhou, Sichuan. Genome assembly was performed using Hifiasm v0.25.0-r726, and the mitochondrial genome of the female duck was assembled using GetOrganelle v1.7.7.1. Using the Minigraph-Cactus pipeline (v3.1.2-gpu) with the Kaijiang female duck as the reference path, we constructed a pangenome (PG-Duck) for other five Chinese local duck breeds, including Pekin duck, Liancheng white duck, Jinding duck, Shaoxing duck, and Longyan Shan-Ma duck. The pangenome spans 1.65 Gb and consists of 55,016,752 nodes and 75,244,230 edges. The data provided in this study include the whole-genome assemblies of both female and male Kaijiang ducks, the annotation file for the female duck, the mitochondrial genome of the female duck, and the graphical pangenome files. This resource enables precise genomics-assisted breeding for traits related to growth, disease resistance, and environmental adaptation in the Dazhou region.KaijiangDuckGenome.tar.gz: KaijiangDuck_MT_Genome.fasta; SASU_KJD_Female_v2.fasta; SASU_KJD_Male_v2.fasta; SASU_KJD_Female_v2_Annotation.gffPG-Duck.tar.gz: panDuck.full.og.tar.gz; panDuck.full.vcf.gz; panDuck.full.gfa.gz; panDuck.full.gbz; panDuck.full.shortread.zipcodes; panDuck.full.shortread.withzip.min; panDuck.full.dist