Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes

Authors

Yan Ren, The University of Adelaide
Callum MacPhillamy, The University of Adelaide
Thu Hien To, Norges Miljø- og Biovitenskapelige Universitet
Timothy P. L. Smith, USDA, Animal Research CenterFollow
John L. Williams, The University of Adelaide
Wai Yee Low, The University of AdelaideFollow

Date of this Version

11-1-2021

Document Type

Article

Citation

Genomics 113 (2021) 3599–3609

https://doi.org/10.1016/j.ygeno.2021.08.021

Comments

This is an open access article under the CC BY license

Abstract

River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.