Supporting data for "Disentangling river- and swamp-buffalo genetic diversity: Initial Insights from the 1000 Buffalo Genomes Project"

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 to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly with substantial resolution of telomeric and centromeric repeats, ~4-fold more contiguous than the existing reference river buffalo assembly (UOA_WB_1) 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 SNPs 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 (Mya) (95% CI: 2.6 to 4.9). Analysis of ~5 million SNPs that were polymorphic in river buffaloes but fixed in swamp buffaloes revealed non-synonymous SNPs in genes such as DGAT1 and KISS1 that were associated with milk and reproductive traits, respectively. The open science model employed in this project (the 1000 buffalo genomes project; 1000BGP) provides a key genomic resource for a species with global economic relevance.