Hanshin D Shin, Wonchoul Park, Han-Ha Chai, Youngho Lee, Jaehoon Jung, Byung June Ko, Heebal Kim
This study presents the first chromosome-level genome assembly of the Korean long-tailed chicken (KLC), a unique breed of Gallus gallus known as Ginkkoridak. Our assembly achieved a super contig N50 of 5.7 Mbp and a scaffold N50 exceeding 90���Mb, with a genome completeness of 96.3% as assessed by BUSCO using the aves_odb10 set. We also constructed a comprehensive pangenome graph, incorporating 40 Gallus gallus assemblies, including the KLC genome. This graph comprises 87,934,214 nodes, 121,720,974 edges, and a total sequence length of 1,709,850,352���bp. Notably, our KLC assembly contributed 1,919,925���bp of new sequences to the pangenome, underscoring the unique genetic makeup of this breed. Furthermore, in comparison with the pangenome, we identified 36,818 structural variants in KLC, which included 2,529 insertions, 27,743 deletions, and 6,546 of either insertions or deletions shorter than 1���kb. We also successfully identified pan-genome wide non-reference sequences. Our KLC assembly and pangenome graph provide valuable genomic resources for studying G. gallus populations.
