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

Thu-Hien To,Yan Ren,Wai Yee Low,John L Williams,Callum Macphillamy,Timothy P.L Smith

doi:10.1016/j.ygeno.2021.08.021

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.

Highlights

The water buffalo (B. bubalis) is a domesticated species that is highly valued as a draft animal and for its meat, milk and hide
We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding
Using the Babesia ovata retrovirus-related Pol poly LINE-1 as search input, we found that this gene is distributed widely across all chromosomes in ruminants (Fig. 5), but is not found in pig or human genomes with filter criteria set to retrieve approximately the full length of Babesia sequence at >90% sequence identity (Fig. S12)

Summary

Introduction

The water buffalo (B. bubalis) is a domesticated species that is highly valued as a draft animal and for its meat, milk and hide. The gene sequence is more amenable to change, which may lead to neo functionalization, subfunctionalization or pseudogenization of the gene Another way a new gene function can emerge is through positive se lection of non-synonymous mutations in existing genes. A variety of methods are available to investigate gene gains and losses [7] and detect beneficial non-synonymous mutations or positively selected sites [8]. The accuracy of these analyses depends on the quality of the genome assemblies available. The probability of error in each base of the genome should be low so that accurate gene models can be developed to detect muta tions that alter the function of protein-coding genes

Methods

Discussion

Conclusion