A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle

Abstract

We generated 73 transcriptomic data of water buffalo, which were integrated with publicly available data in this species, yielding a large dataset of 355 samples representing 20 major tissue categories. We established a multi-tissue gene expression atlas of water buffalo. Furthermore, by comparing them with 4866 cattle transcriptomic data from the cattle genotype–tissue expression atlas (CattleGTEx), we found that the transcriptomes of the two species exhibited conservation in their overall gene expression patterns, tissue-specific gene expression and house-keeping gene expression. We further identified conserved and divergent expression genes between the two species, with the largest number of differentially expressed genes found in the skin, which may be related to structural and functional differences in the skin of the two species. This work provides a source of functional annotation of the buffalo genome and lays the foundations for future genetic and evolutionary studies in water buffalo.

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

“…Interestingly, the non-coding second exon was also not expressed in any of the bison tissues, although it is not affected by the deletion. We then aligned 73 transcriptomic data from 19 tissues from 4 water buffaloes (Si et al, 2023) against the Bos taurus taurus reference sequence. Water buffalo is substantially more diverged from cattle than wisent and bison, but the expression profile of both THRSP exons was similar to cattle with the highest transcript abundance in adipose tissue (9,776 TPM), mammary gland (1,570 TPM), skin (440 TPM), liver (298 TPM), and skeletal muscle (37 TPM) ( Supplementary Fig.…”

“…Publicly available RNA sequencing data from bison (BioProject: PRJNA257088, (Dobson et al, 2021)) and water buffalo (BioProject: PRJNA951806, (Si et al, 2023)) were aligned to the ARS-UCD1.2 assembly and Refseq version 106 annotation with STAR v2.7.9a (Dobin et al, 2013). Integrative Genomics Viewer v2.14.0 (Robinson et al, 2011) was used to visualize the alignments.…”

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

“…Using a combination of genomics and transcriptomics was first proposed by the Functional Annotation of Animal Genomes (FFANG) Consortium to identify the genes that code for proteins that are involved in critical production traits in farm animals 5 . Transcriptomic atlases were generated for common domestic animals such as pigs, cattle, sheep, and chickens [6][7][8][9][10] as well as other species of herbivores such as donkey 11 , water buffalo 12 , and goat 13 . While these published transcriptomic atlases of herbivores are valuable, they are published in independent databases, with no standard protocols for sample collection, RNA sequencing, or data processing.…”