Unraveling the Genetic Legacy of the Korean Long-Tailed Chicken: Chromosome-Level Assembly and Pangenomic Insights

The Korean long-tailed chicken (Ginkkoridak) is a rare breed with extraordinary 1.5-meter tail feathers. Facing near-extinction, this study presents its first chromosome-level genome assembly, plus a 40-genome pangenome, unlocking new insights into Gallus gallus diversity and conservation.
Published in Genetics & Genomics
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About the Article

The Korean long-tailed chicken (KLC), known as “Ginkkoridak,” is an extraordinary breed native to Korea, famous for its strikingly long tail feathers that can grow up to 1.5 meters annually. This breed embodies a rich cultural and biological legacy but faces significant threats to its survival. With fewer than 450 individuals remaining in 2018, the breed has experienced a sharp decline due to the influx of foreign poultry breeds and modernization of agriculture. The genetic distinctiveness and historical importance of KLC underscore the urgent need for detailed genomic research to understand and conserve this unique lineage.

In this study, we present the first chromosome-level genome assembly of KLC, leveraging cutting-edge sequencing technologies. This high-quality assembly is complemented by the creation of a comprehensive pangenome graph incorporating 40 diverse Gallus gallus genome assemblies, showcasing the genomic diversity of the species and the unique characteristics of KLC.

Key Findings

High-Quality Genome Assembly

The chromosome-level genome assembly of KLC achieved a scaffold N50 of over 90 megabase pairs and a genome completeness of 96.3%, as assessed by the BUSCO aves_odb10 dataset. This high level of accuracy and resolution provides a robust foundation for exploring the breed’s genetic traits.

Comprehensive Pangenome Graph

The pangenome graph constructed from 40 Gallus gallus genomes provides unprecedented insights into the genomic diversity of the species. Notably, the KLC assembly alone contributed nearly 1.92 megabase pairs of novel sequences to this graph, highlighting its unique genetic profile.

Structural Variants Unique to KLC

We identified 36,818 variants specific to the KLC genome, including deletions, insertions, and indels. These structural variations likely underpin the KLC’s distinctive phenotype—such as its extraordinarily long tail feathers—and offer a window into the evolutionary history of this breed. By constructing and isolating non-reference sequences across the pangenome, it enabled a new way of comparing similarities and differences among non-reference Gallus gallus breeds.

Future Directions

The KLC genome assembly and its integration into the pangenome graph establish a crucial platform for advancing our understanding of Gallus gallus diversity. As golden standards for constructing pangenome graphs continue to emerge, fully harnessing these methods remains an area of active development, particularly for detecting large-scale genomic rearrangements—such as translocations—beyond the scope of single-reference approaches. The ability to uncover complex structural variants through pangenomes is becoming increasingly relevant as more eukaryotic pangenomes are constructed, opening new avenues for evolutionary and comparative genomics.

Future studies may leverage these resources to investigate the genetic and regulatory elements underpinning the KLC’s remarkable traits, including its extraordinarily long tail feathers. Expanding the pangenome to include additional indigenous breeds and wild relatives of Gallus gallus will provide an even broader perspective on avian genomic variation and evolutionary processes. Moreover, these findings hold practical value for conservation efforts, guiding breeding programs aimed at preserving the genetic integrity of the KLC and other endangered breeds. As genomic tools and single-cell or epigenomic analyses continue to evolve, researchers will be poised to delve even deeper into the genetic regulation and adaptation mechanisms that shape the KLC and other avian species, ultimately helping to safeguard both cultural heritage and biological diversity for future generations.

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Genome
Life Sciences > Biological Sciences > Genetics and Genomics > Genomics > Genome
Structural Variation
Life Sciences > Biological Sciences > Genetics and Genomics > Population Genetics > Genetic Variation > Structural Variation

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