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Open Access Highly Accessed Research article

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

Anna Esteve-Codina12*, Robert Kofler3, Nicola Palmieri3, Giovanni Bussotti4, Cedric Notredame4 and Miguel Pérez-Enciso125

Author affiliations

1 Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain

2 Center for Research in Agricultural Genomics (CRAG), Campus UAB, 08193 Bellaterra, Spain

3 Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria

4 Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Carrer del Doctor Aiguader 88, Barcelona, Spain

5 Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, 08010 Barcelona, Spain

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Citation and License

BMC Genomics 2011, 12:552  doi:10.1186/1471-2164-12-552

Published: 8 November 2011

Abstract

Background

Although RNA-seq greatly advances our understanding of complex transcriptome landscapes, such as those found in mammals, complete RNA-seq studies in livestock and in particular in the pig are still lacking. Here, we used high-throughput RNA sequencing to gain insight into the characterization of the poly-A RNA fraction expressed in pig male gonads. An expression analysis comparing different mapping approaches and detection of allele specific expression is also discussed in this study.

Results

By sequencing testicle mRNA of two phenotypically extreme pigs, one Iberian and one Large White, we identified hundreds of unannotated protein-coding genes (PcGs) in intergenic regions, some of them presenting orthology with closely related species. Interestingly, we also detected 2047 putative long non-coding RNA (lncRNA), including 469 with human homologues. Two methods, DEGseq and Cufflinks, were used for analyzing expression. DEGseq identified 15% less expressed genes than Cufflinks, because DEGseq utilizes only unambiguously mapped reads. Moreover, a large fraction of the transcriptome is made up of transposable elements (14500 elements encountered), as has been reported in previous studies. Gene expression results between microarray and RNA-seq technologies were relatively well correlated (r = 0.71 across individuals). Differentially expressed genes between Large White and Iberian showed a significant overrepresentation of gamete production and lipid metabolism gene ontology categories. Finally, allelic imbalance was detected in ~ 4% of heterozygous sites.

Conclusions

RNA-seq is a powerful tool to gain insight into complex transcriptomes. In addition to uncovering many unnanotated genes, our study allowed us to determine that a considerable fraction is made up of long non-coding transcripts and transposable elements. Their biological roles remain to be determined in future studies. In terms of differences in expression between Large White and Iberian pigs, these were largest for genes involved in spermatogenesis and lipid metabolism, which is consistent with phenotypic extreme differences in prolificacy and fat deposition between these two breeds.