A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing

Abstract

BackgroundElucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.ResultsHere we used massive parallel high-throughput RNA sequencing to generate a high-resolution map of the porcine mRNA and miRNA transcriptome in liver, longissimus dorsi and abdominal fat from two full-sib F2 hybrid pigs with segregated phenotypes on growth, blood physiological and biochemical parameters, and fat deposition. We obtained 8,508,418-10,219,332 uniquely mapped reads that covered 78.0% of the current annotated transcripts and identified 48,045-122,931 novel transcript fragments, which constituted 17,085-29,499 novel transcriptional active regions in six tested samples. We found that about 18.8% of the annotated genes showed alternative splicing patterns, and alternative 3' splicing is the most common type of alternative splicing events in pigs. Cross-tissue comparison revealed that many transcriptional events are tissue-differential and related to important biological functions in their corresponding tissues. We also detected a total of 164 potential novel miRNAs, most of which were tissue-specifically identified. Integrated analysis of genome-wide association study and differential gene expression revealed interesting candidate genes for complex traits, such as IGF2, CYP1A1, CKM and CES1 for heart weight, hemoglobin, pork pH value and serum cholesterol, respectively.ConclusionsThis study provides a global view of the complexity of the pig transcriptome, and gives an extensive new knowledge about alternative splicing, gene boundaries and miRNAs in pigs. Integrated analysis of genome wide association study and differential gene expression allows us to find important candidate genes for porcine complex traits.

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

“…In similar studies of pigs (Chen et al, 2011;Esteve-Codina et al, 2011) and cattle (Huang et al, 2012), in which 61.6-77.8% of reads were matched to the reference genome, our results were comparable for sheep. The percentage of reads mapped to the reference genes were lower than that mapped to the O. aries genome, a result potentially due to the GC content, type of cells, and other reasons (McIntyre et al, 2011;Sendler et al, 2011).…”

“…The most common AS identified in our research was IR, in both Mongolian and Lanzhou fat-tailed sheep. Our results were similar to those for rice (Zhang et al, 2010), but different from those for pigs (Chen et al, 2011) and Dorper and small-tailed Han sheep (Zhang et al, 2013), in which A3SS was identified as the most common AS. Our results also differed from those of humans (Sultan et al, 2008), in which ES was the primary type of AS.…”

Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep

“…1B). Compared with the reports for non-model organisms of sheep [13], pigs [4] and bovine [31], in which 61.4e75.0% of reads mapped to the reference genome, our mapping percentage was pretty comparable and even better, which are ensuring reliable downstream analysis.…”

MicroRNA-877 acts as a tumor suppressor by directly targeting eEF2K in renal cell carcinoma

“…It has been demonstrated that miRNAs are stable and resistant to extreme pH and temperature in body fluids (29,30), and serum miRNAs have been reported as the best biomarker for cancer diagnosis (31,32). Thus, the use of serum as a diagnostic tool for patients with RCC is of relevance.…”