ArticleBMC genomics2012
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio).
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 120 citations in OpenAlex.
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- Expression profiles and functional characterization of common carp (Biochemistry and biophysics reports · 2021Article
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- Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae.Science China. Life sciences · 2021Article
- Transposable Elements and Teleost Migratory Behaviour.International journal of molecular sciences · 2021Article
- Insights into the Function and Evolution of Taste 1 Receptor Gene Family in the Carnivore Fish Gilthead Seabream (International journal of molecular sciences · 2020Article
- Mobile Elements in Ray-Finned Fish Genomes.Life (Basel, Switzerland) · 2020Review
- Genome-wide comparative analysis ofbone morphogenetic proteins: genomic structure, phylogeny, and expression patterns in the golden pompano,Trachinotus ovatus(Linnaeus, 1758).Fish physiology and biochemistry · 2020Article
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- Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes.Journal of molecular evolution · 2019Article
- A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus).BMC genomics · 2018Article
- Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCommon 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.
resultsWe 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.
conclusionsThe 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.
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