Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis

Wenli Li,Derek M Bickhart,Luigi Ramunno,Daniela Iamartino,John L Williams,George E Liu

doi:10.1016/j.dib.2018.05.015

Abstract

Water buffalo (Bubalus bubalis L.) is an important livestock species worldwide. Like many other livestock species, water buffalo lacks high quality and continuous reference genome assembly, required for fine-scale comparative genomics studies. In this work, we present a dataset, which characterizes genomic differences between water buffalo genome and the extensively studied cattle (Bos taurus Taurus) reference genome. This data set is obtained after alignment of 14 river buffalo whole genome sequencing datasets to the cattle reference. This data set consisted of 13,444 deletion CNV regions, and 11,050 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Gene expression data from cattle and buffalo were also presented for genes impacted by these regions. Public assessment of this dataset will allow for further analyses and functional annotation of genes that are potentially associated with phenotypic difference between cattle and water buffalo.

Highlights

Water buffalo (Bubalus bubalis L.) is an important livestock species worldwide
We present a dataset, which characterizes genomic differences between water buffalo genome and the extensively studied cattle (Bos taurus Taurus) reference genome
This data set consisted of 13,444 deletion CNV regions, and 11,050 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes

Summary

Data used and experimental design

Genomic DNA samples from river buffalo were provided by the International Water Buffalo Genome Consortium. Sequence data was generated at the USDA Agricultural Research Service (Beltsville) on an Illumina Genome Analyzer II. All sequencing data were submitted to NCBI (accession #PRJNA350833). Genomic sequencing reads from cattle were deposited to NCBI (accession #PRJNA277147). For whole transcriptome sequencing data, raw reads of river buffalo tissue transcriptomics were deposited to NCBI (accession #PRJEB4351). This study used the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons between river buffalo and cattle, by aligning whole genome shotgun sequencing reads from river buffalo to the cattle reference genome. To identify river buffalo specific, genomic variants, CNV, SNP and MEI calls resulting from the cattle WGS reads were used as a background filter to remove variant sites previously identified in cattle from the river buffalo dataset

Structural variant calling

Comparative gene expression analysis between cattle and river buffalo