Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project

Paulene S Pineda, Ester B Flores, Lilian P Villamor, Connie Joyce M Parac, Mehar S Khatkar, Hien To Thu, Timothy P. L Smith, Benjamin D Rosen, Paolo Ajmone Marsan, Licia Colli, John L Williams, John Lewis Williams, Wai Yee Low, Lloyd Low, Mehar Khatkar, Tong Chen, Hanh Thi Hong Nguyen, Humberto Tonhati, Gregório Miguel Ferreira De Camargo, Stefano BiffaniJianlin Han, Yi Zhang, Mei Liu, Yang Zhou, Divier Antonio Agudelo Gómez, P. Kumarasamy, Jaswinder Singh Bhatti, Manishi Mukesh, Dwi Sendi Priyono, Akhmad Dakhlan, Mahdi Mokhber, John Williams, Ajmone Marsan Paolo, Mayra Gómez Carpio, Roberta Cimmino, Ali Raza Awan, Connie Joyce Parac, Rangsun Parnpai, Siri Tuk, M. Ihsan Soysal, Emel Özkan Unal, Raziye Isik, Zhihua Jiang, Lu'C Dô Du'C, Nguyen Hoang Thinh

Risultato della ricerca: Contributo in rivistaArticolo in rivista

Abstract

More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and tools to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly (PCC-UOA-SB-1v2) with substantial resolution of telomeric and centromeric repeats, ∼4-fold more contiguous than the existing reference river buffalo assembly and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ∼41 million single nucleotide polymorphisms per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ∼1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (95% CI, 2.6-4.9). The open science model employed in the 1000BGP provides a key genomic resource and tools for a species with global economic relevance.
Lingua originaleEnglish
pagine (da-a)1-14
Numero di pagine14
RivistaGigaScience
Volume2024
DOI
Stato di pubblicazionePubblicato - 2024

Keywords

  • SNP panel
  • buffalo genomics
  • carabao
  • structural variants
  • whole-genome sequencing

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