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

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.

Figure 1

A bar plot showing the hits to protein sequences from five sequenced teleost species. Alignments of common carp contigs to protein sequences from Zebrafish, Fugu, Stickleback, Tetraodon and Medaka, respectively.

Figure 2

Ks value distribution to identify the genome duplication event and the speciation event. Data was grouped into bins of 0.01 Ks units for graphing. For common carp and zebrafish, the Ks distributions of duplication events were shown in red and green respectively. A secondary Ks peak within common carp indicated the genome duplication (red line). Given the rate of substitutions/synonymous site per year, the peak indicated the time of the 4R of genome duplication. Within zebrafish, no secondary peak in the Ks distribution of paralogous sequences was observed (green line). The Ks distribution of the orthologous pairs was plotted in blue line and showed a distinct secondary Ks peak, indicating the speciation time between these two species.

Figure 3

Distribution of common carp GO terms in biological process and molecular function categories. The relative proportion of GO terms is represented by more than 100 contigs for the biological process (A) and molecular function (B) categories in the GO vocabulary. The enriched GO terms in common carp (p < 0.05) were highlighted with orange.