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.
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project / Pineda, Paulene S; Flores, Ester B; Villamor, Lilian P; Parac, Connie Joyce M; Khatkar, Mehar S; Thu, Hien To; Smith, Timothy P L; Rosen, Benjamin D; Ajmone-Marsan, Paolo; Colli, Licia; Williams, John L; Low, Wai Yee; Null, Null; Low, Lloyd; Khatkar, Mehar; Chen, Tong; Nguyen, Hanh Thi Hong; Tonhati, Humberto; de , ; Camargo, Gregório Miguel Ferreira; Biffani, Stefano; Han, Jianlin; Zhang, Yi; Liu, Mei; Zhou, Yang; Gómez, Divier Antonio Agudelo; Kumarasamy, P; Bhatti, Jaswinder Singh; Mukesh, Manishi; Priyono, Dwi Sendi; Dakhlan, Akhmad; Mokhber, Mahdi; Williams, John; Paolo, Ajmone Marsan; Colli, Licia; Carpio, Mayra Gómez; Cimmino, Roberta; Awan, Ali Raza; Pineda, Paulene S; Villamor, Lilian P; Flores, Ester B; Parac, Connie Joyce; Parnpai, Rangsun; Tuk, Siri; Soysal, M İhsan; Unal, Emel Özkan; Isik, Raziye; Jiang, Zhihua; Lụ'C, Ðỗ Ðụ'C; Thinh, Nguyen Hoang. - In: GIGASCIENCE. - ISSN 2047-217X. - 13:(2024). [10.1093/gigascience/giae053]
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
Biffani, Stefano;
2024-01-01
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
