@article{8ee3d898bdc24fc68d30b85d31e865ec,
title = "Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project",
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.",
keywords = "SNP panel, buffalo genomics, carabao, structural variants, whole-genome sequencing, SNP panel, buffalo genomics, carabao, structural variants, whole-genome sequencing",
author = "Pineda, {Paulene S} and Flores, {Ester B} and Villamor, {Lilian P} and Parac, {Connie Joyce M} and Khatkar, {Mehar S} and Thu, {Hien To} and Smith, {Timothy P. L} and Rosen, {Benjamin D} and {Ajmone Marsan}, Paolo and Licia Colli and Williams, {John L} and Williams, {John Lewis} and Low, {Wai Yee} and Lloyd Low and Mehar Khatkar and Tong Chen and Nguyen, {Hanh Thi Hong} and Humberto Tonhati and {De Camargo}, {Greg{\'o}rio Miguel Ferreira} and Stefano Biffani and Jianlin Han and Yi Zhang and Mei Liu and Yang Zhou and G{\'o}mez, {Divier Antonio Agudelo} and P. Kumarasamy and Bhatti, {Jaswinder Singh} and Manishi Mukesh and Priyono, {Dwi Sendi} and Akhmad Dakhlan and Mahdi Mokhber and John Williams and Paolo, {Ajmone Marsan} and Carpio, {Mayra G{\'o}mez} and Roberta Cimmino and Awan, {Ali Raza} and Parac, {Connie Joyce} and Rangsun Parnpai and Siri Tuk and Soysal, {M. Ihsan} and Unal, {Emel {\"O}zkan} and Raziye Isik and Zhihua Jiang and {D{\^o} Du'C}, Lu'C and Thinh, {Nguyen Hoang}",
year = "2024",
doi = "10.1093/gigascience/giae053",
language = "English",
volume = "2024",
pages = "1--14",
journal = "GigaScience",
issn = "2047-217X",
publisher = "Oxford University Press",
}