A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

Abstract

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

“…Overall, the identified DEGs in multiple core tissues between beef and dairy cattle should enable our understanding of their transcriptional regulation on development and functional differentiation of tissue. In addition, our study further supports tissue-specific regulatory patterns which are consistent with the action of natural selection across species, as described in passerine birds [ 110 ], primates [ 111 ], and high-altitude vertebrates [ 112 ], and help to understand the genomic variation and their regulations in diverse breeds that may reflect differences in production traits [ 4 , 27 , 113 ].…”

Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages

“…Graphia is a computational tool which enables the analysis and visualization of large correlation networks. Amongst many applications it was used to identify cell and tissue-specific co-expression clusters in the sheep ( Clark et al, 2017 ), pig ( Summers et al, 2019 ) goat ( Muriuki et al, 2019 ), water buffalo ( Young et al, 2019 ), and chicken ( Bush et al, 2018a ) transcriptional atlas projects. Co-expression analysis of a detailed time course of the transcriptomic response of human MDM to LPS treatment based upon sequencing of CAGE (genome scale 5′ RACE) libraries revealed the transient induction of positive and negative regulators ( Baillie et al, 2017 ).…”

Transcriptome Atlas of 16 Donkey Tissues

“…In addition, the brain and the testis exhibited a higher percentage of tissue-enriched proteins, which were also found in human ( Uhlén et al, 2015 ; Wang et al, 2019 ), cattle ( Liu et al, 2020 ), sheep ( Clark et al, 2017 ), and goat ( Muriuki et al, 2019 ), than other organs. The result of the functional analysis showed that brain-enriched genes were significantly associated with synapse and neuron function and testis-enriched genes with spermatogenesis and reproduction in humans ( Wang et al, 2019 ), cattle ( Liu et al, 2020 ), and donkey.…”

“…One cattle transcriptome study showed that 16,564 genes were detected by analyzing 100 different tissues and cell types ( Liu et al, 2020 ). In addition, approximately 18,528, 19,921, and 14,426 protein-coding genes were detected in domestic goat ( Muriuki et al, 2019 ), sheep ( Clark et al, 2017 ), and pig ( Freeman et al, 2012 ), respectively. The number of detected genes in donkey is equivalent to that in cattle.…”

“…Identified by the same method, approximately 6,700 and 9,000 ubiquitously expressed housekeeping genes were observed in donkey and humans ( Uhlén et al, 2015 ), respectively. The housekeeping genes identified by a cluster analysis in sheep ( Clark et al, 2017 ), goat ( Muriuki et al, 2019 ), and pig ( Freeman et al, 2012 ) were also clustered into several largest clusters. Housekeeping genes are fundamental to maintain essential cellular structure and function.…”