Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

Abstract

Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Cyprinus carpio L.)

“…The microRNA target prediction tool psRNAtarget (V2, 2017 release) ( http://plantgrn.noble.org/psRNATarget/ ) ( Dai and Zhao, 2011 ) was used to carry out an analysis of the interactions between lncRNA-miRNA and miRNA-mRNA ( Zhou et al, 2021 ; Khan et al, 2022 ). Identified common carp lncRNAs corresponding miRNA were taken from previous studies ( Wang et al, 2017a ) while the mRNAs data were retrieved from NCBI database.…”

Whole Genome Sequencing and Assembly of Bangladeshi Native Cattle, Mirkadim

“…Revealing the genetic makeup of this breed can help to decipher genetic variants or genotypes that can increase meat production in the near future by selective breeding or genome editing [2]. Previously, the whole genome sequence of Water Buffalo (Bubalus bubalis) and indigenous Red Chittagong Cattle (RCC) cattle were sequenced in Bangladesh [3,4]. However, the genomic composition of the popular Mirkadim breed was unknown.…”