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

Authors: Li, Wenli; Bickhart, Derek; RAMUNNO, LUIGI - Universita Di Napoli; IAMARTINO, DANIELA - Parco Tecnologico Padano; WILLIAMS, JOHN - University Of Adelaide; Liu, Ge - George

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2018
Publication Date: 2/28/2018
Citation: Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J., Liu, G. 2018. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics. https://doi.org/10.1016/j.ygeno.2018.02.018.

Interpretive Summary: Water buffalo represent a significant livestock species in many parts of the world, with high economic importance and promising characteristics for the production of milk and meat; however, like many other livestock species, they lack a highly polished and contiguous reference genome assembly for use in high-resolution comparative genomics studies. This study sought to characterize differences in gene content, regulation, and structure between taurine cattle and water buffalo by using the extensively annotated UMD3.1 cattle reference genome as a basis for all sequence-based comparisons. Our comparative alignment approach and comparative gene expression analysis suggests a functional role for many genomic structural variations, which may contribute to the unique phenotypes of water buffalo. This information will be useful for future functional follow-up on genetic contributors associated with production traits in water buffalo.

Technical Abstract: Water buffalo (Bubalus bubalis L.) represent a significant livestock species with high economic importance and promising characteristics for production; however, like many other livestock species, they lack a highly polished and contiguous reference genome assembly for use in high-resolution comparative genomics studies. This study sought to characterize differences in gene content, regulation and structure between taurine cattle and water buffalo by using the extensively annotated UMD3.1 cattle reference genome as a basis for all sequence-based comparisons. After alignment of 14 WGS water buffalo WGS datasets to the cattle reference, we identified 127 deletion CNV regions that are present in at least 13 investigated buffalo individuals, representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion events (MEI) within the upstream regions of annotated cattle genes. These MEIs intersected with 70 Ensembl annotated cattle genes. To assess the functional impact of the structural differences identified in our study, we performed comparative gene expression analysis between Angus cattle and buffalo using publicly available RNA-sequencing data. Transcriptome analysis in various tissue types in water buffalo confirmed the absence of 4 cattle genes that are predicted to be completely deleted in buffalo. Three genes with upstream MEI predictions were found to have significant differential expression in water buffalo compared to cattle and may be related to phenotypic differences in meat quality and color. Our comparative alignment approach and comparative gene expression analysis suggests a functional role for many genomic structural variations, which may contribute to the unique phenotypes of water buffalo.