Near telomere-to-telomere assembly of the Tarim pigeon (Columba livia) genome

Wenhao Yang; Hao Zhou; Jinlong Huang; Wenqi Zhu; Haobin Hou; Hejun Li; Lele Zhao; Jiang Zhang; Jiajia Liu; Chao Qin; Liyuan Wang; Huaixi Luo; Jianshen Zhu; Fuquan Xiao; Junfeng Yao; Changsuo Yang; He Meng

doi:10.1038/s41597-024-04350-5

Near telomere-to-telomere assembly of the Tarim pigeon (Columba livia) genome

Sci Data. 2024 Dec 31;11(1):1455. doi: 10.1038/s41597-024-04350-5.

Authors

Wenhao Yang¹, Hao Zhou¹, Jinlong Huang^{1

2}, Wenqi Zhu¹, Haobin Hou³, Hejun Li⁴, Lele Zhao⁴, Jiang Zhang⁴, Jiajia Liu¹, Chao Qin¹, Liyuan Wang¹, Huaixi Luo¹, Jianshen Zhu¹, Fuquan Xiao¹, Junfeng Yao⁵, Changsuo Yang⁶, He Meng⁷

Affiliations

¹ Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
² School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
³ Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
⁴ Shanghai Vocational College of Agriculture and Forestry, Shanghai, 201699, China.
⁵ Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China. [email protected].
⁶ Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China. [email protected].
⁷ Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. [email protected].

Abstract

Pigeons serve as important model animals and commercial poultry. The Tarim pigeon, as a breed of Columba livia, is a locally indigenous breed unique to China. While the genome of C. livia was published in 2013, its assembly was fragmented and incomplete. In this study, we generated a near telomere-to-telomere assembly of the pigeon genome using the sequencing platform of PacBio HiFi, Nanopore long reads and Hi-C. The assembled genome spans 1295.8 Mb, with a contig N50 size of 49 Mb and a scaffold N50 size of 85 Mb. Approximately 98.4% of the assembly is anchored onto 41 chromosomes, with a BUSCO assessment indicating a completeness of 97.2%. And telomeres were identified at both ends of the four chromosomes. A total of 21,450 genes were annotated. The genome assembly of C. livia lays the foundation for understanding their genetic composition and evolutionary history and contributes to the pigeon breeding industry. Additionally, it will provide a basis for further management and conservation of pigeon breed diversity.

Publication types

Dataset

MeSH terms

Animals
Columbidae* / genetics
Genome*
Telomere* / genetics