Abstract
The pig (Sus scrofa) is not only an important livestock animal but also widely used as a biomedical model. However, the understanding of the molecular characteristics of organs and of the developmental skeletal muscle of the pig is severely limited. Here, we performed a comprehensive transcriptome profiling of mRNAs and miRNAs across nine tissues and three skeletal muscle developmental stages in the Guizhou miniature pig. The reproductive organs (ovary and testis) had greater transcriptome complexity and activity than other tissues, and the highest transcriptome similarity was between skeletal muscle and heart (R = 0.79). We identified 1,819 mRNAs and 96 miRNAs to be tissue-specific in nine organs. Testis had the largest number of tissue-specific mRNAs (992) and miRNAs (40). Only 15 genes and two miRNAs were specifically expressed in skeletal muscle and fat, respectively. During postnatal skeletal muscle development, the mRNAs associated with focal adhesion, Notch signaling, protein digestion, and absorption pathways were up-regulated from D0 to D30 and then down-regulated from D30 and D240, while genes with opposing expression patterns were significantly enriched in the oxidative phosphorylation and proteasome pathways. The miRNAs mainly regulated genes associated with insulin, Wnt, fatty acid biosynthesis, Notch, MAPK, TGF-beta, insulin secretion, ECM–receptor interaction, focal adhesion, and calcium signaling pathways. We also identified 37 new miRNA–mRNA interaction pairs involved in skeletal muscle development. Overall, our data not only provide a rich resource for understanding pig organ physiology and development but also aid the study of the molecular functions of mRNA and miRNA in mammals.
Highlights
Intensive transcriptome sequencing is increasingly being used to study the mechanisms of organ physiology and development, with a goal of understanding the genetic expressions of tissuespecific diseases (Lage et al, 2008; Koh et al, 2014)
The smallest numbers of expressed protein coding genes (PCGs) were in skeletal muscle and the largest numbers were in the reproductive tissues
Gene Ontology (GO) terms for muscle tissue development were significantly enriched in skeletal muscle and heart, while the genes associated with spermatogenesis, lipid metabolism, and immune response were enriched in testis, adipose, and spleen, respectively
Summary
Intensive transcriptome sequencing is increasingly being used to study the mechanisms of organ physiology and development, with a goal of understanding the genetic expressions of tissuespecific diseases (Lage et al, 2008; Koh et al, 2014). Tissue-specific expression of both protein-coding and non-coding RNAs in both humans and mice has been well studied (Roux et al, 2012; Szabo et al, 2015; Zeng et al, 2016; Iwakiri et al, 2017) and the results have been used to elucidate organ physiologies and diseases. While many studies have accumulated both mouse and human tissue-specific transcriptome data (Zhang et al, 2015a), RNA-seq transcriptome analyses across tissues and developmental stages of other mammals are still relatively scarce
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