Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies
Abstract 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 assess...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04287-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841544995485515776 |
|---|---|
| author | Hanshin D. Shin Wonchoul Park Han-ha Chai Youngho Lee Jaehoon Jung Byung June Ko Heebal Kim |
| author_facet | Hanshin D. Shin Wonchoul Park Han-ha Chai Youngho Lee Jaehoon Jung Byung June Ko Heebal Kim |
| author_sort | Hanshin D. Shin |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-b15be6cbd17b4adf9a01de51e8c6a41b |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-b15be6cbd17b4adf9a01de51e8c6a41b2025-01-12T12:07:38ZengNature PortfolioScientific Data2052-44632025-01-0112111010.1038/s41597-024-04287-9Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus AssembliesHanshin D. Shin0Wonchoul Park1Han-ha Chai2Youngho Lee3Jaehoon Jung4Byung June Ko5Heebal Kim6Interdisciplinary Program in Bioinformatics, Seoul National UniversityAnimal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA 1500Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA 1500Interdisciplinary Program in Bioinformatics, Seoul National UniversityDepartment of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National UniversityInterdisciplinary Program in Bioinformatics, Seoul National UniversityAbstract 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.https://doi.org/10.1038/s41597-024-04287-9 |
| spellingShingle | Hanshin D. Shin Wonchoul Park Han-ha Chai Youngho Lee Jaehoon Jung Byung June Ko Heebal Kim Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies Scientific Data |
| title | Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies |
| title_full | Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies |
| title_fullStr | Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies |
| title_full_unstemmed | Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies |
| title_short | Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies |
| title_sort | chromosome level genome assembly of korean long tailed chicken and pangenome of 40 gallus gallus assemblies |
| url | https://doi.org/10.1038/s41597-024-04287-9 |
| work_keys_str_mv | AT hanshindshin chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT wonchoulpark chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT hanhachai chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT youngholee chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT jaehoonjung chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT byungjuneko chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies AT heebalkim chromosomelevelgenomeassemblyofkoreanlongtailedchickenandpangenomeof40gallusgallusassemblies |