Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle

Authors: Li, Wenli; Bickhart, Derek; LAMARTINO, DANIELA - Laboratorio Di Genetica E Servizi (LGS); RAMUNNO, LUIGI - Dipartimento Di Agraria, Universita Degli Studi Di Sassari; WILLIAMS, JOHN - University Of Adelaide; Liu, Ge - George

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/19/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Water buffalo (Bubalus bubalis L.) is a significant livestock species worldwide with high economic importance. There are distinct phenotypic differences between taurine cattle and water buffalo, and the variations in the gene content and gene copy number between these two species are key contributors to such phenotypic differences. In this study, using cattle genome as the reference and the next-generation sequencing reads generated for 14 water buffalo individuals, we performed genome wide analysis to identify gene copy number variations (CNVs), single nucleotide variants and mobile elements insertions (MEIs) events unique to water buffalo. In total, we found 27 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 MEI events within the upstream regions of annotated cattle genes. Using whole transcriptome sequencing data, we successfully confirmed the significantly increased expression of four genes in water buffalo, for which upstream MEI predictions were identified.

Technical Abstract: This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (one subspecies of domestic water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. We identified 127 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Transcriptome analysis in various tissue types on river buffalo confirmed the absence of four cattle genes. Four genes which may be related to phenotypic differences in meat quality and color, had upstream MEI predictions and were found to have significantly elevated expression in river buffalo compared with cattle. Our comparative alignment approach and gene expression analyses suggested a functional role for many genomic structural variations, which may contribute to the unique phenotypes of river buffalo.