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本数据集整合了牛津纳米孔测序（ONT）、高保真测序（HiFi）、Hi-C及下一代测序（NGS）技术，成功构建了连续性优异的端粒到端粒（T2T）级雌性鸭参考基因组，以及四川达州地理标志产品——开江公鸭的染色体级参考基因组。基因组组装采用Hifiasm v0.25.0-r726完成，雌性鸭线粒体基因组则通过GetOrganelle v1.7.7.1组装获得。本研究以开江雌性鸭为参考路径，借助Minigraph-Cactus流程（v3.1.2-gpu），构建了涵盖北京鸭、连城白鸭、金定鸭、绍兴鸭、龙岩山麻鸭5个中国地方鸭品种的泛基因组（PG-Duck）。该泛基因组全长1.65 Gb，包含55,016,752个节点与75,244,230条边。本研究提供的数据包括雌性与雄性开江鸭的全基因组组装结果、雌性鸭的基因组注释文件、雌性鸭线粒体基因组，以及图形化泛基因组文件。该数据集资源可用于达州地区鸭只生长、抗病及环境适应性相关性状的精准基因组辅助育种。 KaijiangDuckGenome.tar.gz: KaijiangDuck_MT_Genome.fasta; SASU_KJD_Female_v2.fasta; SASU_KJD_Male_v2.fasta; SASU_KJD_Female_v2_Annotation.gff PG-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