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Open Access Research article

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

Jin-Tu Wang12, Jiong-Tang Li1*, Xiao-Feng Zhang3 and Xiao-Wen Sun1*

Author affiliations

1 The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China

2 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China

3 Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haerbin 150070, China

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Citation and License

BMC Genomics 2012, 13:96  doi:10.1186/1471-2164-13-96

Published: 19 March 2012

Abstract

Background

Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event.

Results

We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp.

Conclusions

The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.

Keywords:
Sequence assembly; Genome duplication; Common carp; Substitution rate; Speciation