Transcriptome Atlas of 16 Donkey Tissues.

Yinan Wang,Changfa Wang,Xinyao Miao,Zicheng Zhao,Shuaicheng Li,Yonghui Wang

doi:10.3389/fgene.2021.682734

Yinan Wang, Changfa Wang + Show 4 more

Open Access

https://doi.org/10.3389/fgene.2021.682734

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Abstract

Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits.

Highlights

Donkeys (Equus asinus) are one of the most common species in agricultural production and transportation (Polidori et al, 2015), with considerable commercial and economic value in meat, skin, and milk production (Camillo et al, 2018; Zhang et al, 2020)
Sixteen histologically healthy tissue specimens representing major donkey organs were analyzed by RNA sequencing (Table 1)
transcripts per million (TPM) was used as a measure of gene expression

Summary

Introduction

Donkeys (Equus asinus) are one of the most common species in agricultural production and transportation (Polidori et al, 2015), with considerable commercial and economic value in meat, skin, and milk production (Camillo et al, 2018; Zhang et al, 2020). In Asia, donkey skin and meat contributed to food and healthy productions (Camillo et al, 2018; Zhang et al, 2020). China produces approximately 0.27 million tons of donkey milk annually (Luo et al, 2019) and has a long history of alimentary and medicinal usage of donkey milk (Li et al, 2018)

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