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Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery.

ABSTRACT: Pig (Sus scrofa) is an important organism for both agricultural and medical purpose. This study aims to investigate the S. scrofa transcriptome by the use of Roche 454 pyrosequencing. We obtained a total of 558 743 and 528 260 reads for the back-leg muscle and ovary tissue each. The overall 1 087 003 reads give rise to 421 767 341 bp total residues averaging 388 bp per read. The de novo assemblies yielded 11 057 contigs and 60 270 singletons for the back-leg muscle, 12 204 contigs and 70 192 singletons for the ovary and 18 938 contigs and 102 361 singletons for combined tissues. The overall GC content of S. scrofa transcriptome is 42.3% for assembled contigs. Alternative splicing was found within 4394 contigs, giving rise to 1267 isogroups or genes. A total of 56 589 transcripts are involved in molecular function (40 916), biological process (38 563), cellular component (35 787) by further gene ontology analyses. Comparison analyses showed that 336 and 553 genes had significant higher expression in the back-leg muscle and ovary each. In addition, we obtained a total of 24 214 single-nucleotide polymorphisms and 11 928 simple sequence repeats. These results contribute to the understanding of the genetic makeup of S. scrofa transcriptome and provide useful information for functional genomic research in future.

SUBMITTER: Nie Q

PROVIDER: S-EPMC3190955 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs).One genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives.This work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin.

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Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery.

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