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Transcriptomic analysis of Rongchang pig brains and livers

ABSTRACT: Recent developments in high-throughput RNA sequencing (RNA-seq) technology have had a dramatic impact on our comprehension of the structure and expression profiles of the mammalian transcriptome. This study performed transcriptome analysis of Rongchang pig brains and livers using deep RNA-seq technology to offer insights into potential swine genetic improvements, in addition to examining the use of the Rongchang pig as a biomedical model.By sequencing the mRNA of two extreme tissues, brains and livers, a total of 8.6 Gb of sequencing was obtained, with 91% resulting in clean reads, with approximately 43 million reads from the brain and 44 million reads from the liver samples. This analysis revealed tissue specificity through the identification of 5,575 and 4,600 differentially expressed genes (DEGs) in brains and livers respectively. Functional analysis of the differentially expressed genes showed that the top ten functional pathways with highly enriched gene expression in brains were associated with nerves, while in livers the pathways were predominantly related to metabolism. Furthermore, 83 neuropeptide gene transcripts, 69 neuropeptide receptor gene transcripts, 10 pro-neuropeptide convertase gene transcripts, 12 insulin-like growth factors binding protein gene transcripts, and other neuropeptide related protein gene transcripts were identified, to reveal different expression profiles in brain and liver samples. In this study, major characteristics of the transcriptional profiles of Rongchang pig brains and livers were present. Overall, our data provides useful information for future research pertaining to swine livestock and biomedical research.

ORGANISM(S): Sus scrofa

PROVIDER: GSE54093 | GEO | 2015/07/30

SECONDARY ACCESSION(S): PRJNA235171

REPOSITORIES: GEO

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Project description:Purpose: The goal of this study was to perform a transcriptome-wide analysis of variation in brain gene expression between domesticated pig and wild boars using illumina sequencing strategy. Methods: Brain mRNA profiles of wild boars and Rongchang pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: First, we totally identified 20,805 genes in two groups, of which 18,904 in wild boar and 17,980 in Rongchang pigs, respectively. Second, we detected substantial variation in expression profiles between wild boar and Rongchang pig, including substantial wild boar/Rongchang specifically expressed genes and differentially expressed genes. The functional enrichment analysis revealed immune response was enriched for genes upregulated in wild boars. Finally, we compared our results against previous study and identified seven genes that were associated with domestication.The work performed here will provide a typical demonstration for future deciphering the mechanism of pig domestication.

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Transcriptomic analysis of Rongchang pig brains and livers

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