Genome sequence and genetic diversity of the common carp, Cyprinus carpio

FAO Fisheries and Aquaculture Department. The State of World Fisheries and Aquaculture 2006 (Food and Agriculture Organization of the United Nations, Rome, 2007).

Bostock, J. et al. Aquaculture: global status and trends. Phil. Trans. R. Soc. B 365, 2897–2912 (2010).

Hinegardner, R. & Rosen, D.E. Cellular DNA content and the evolution of teleostean fishes. Am. Nat. 106, 621–644 (1972).

Wang, J.T., Li, J.T., Zhang, X.F. & Sun, X.W. Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). BMC Genomics 13, 96 (2012).

David, L., Blum, S., Feldman, M.W., Lavi, U. & Hillel, J. Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. Mol. Biol. Evol. 20, 1425–1434 (2003).

Ohno, S., Muramoto, J., Christian, L. & Atkin, N.B. Diploid-tetraploid relationship among old-world members of the fish family Cyprinidae. Chromosoma 23, 1–9 (1967).

Larhammar, D. & Risinger, C. Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio. Mol. Phylogenet. Evol. 3, 59–68 (1994).

Ji, P. et al. High throughput mining and characterization of microsatellites from common carp genome. Int. J. Mol. Sci. 13, 9798–9807 (2012).

Xu, J. et al. Genome-wide SNP discovery from transcriptome of four common carp strains. PLoS ONE 7, e48140 (2012).

Zhang, X. et al. A consensus linkage map provides insights on genome character and evolution in common carp (Cyprinus carpio L.). Mar. Biotechnol. (NY) 15, 275–312 (2013).

Zheng, X. et al. A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs. Mol. Genet. Genomics 286, 261–277 (2011).

Zhang, Y. et al. Genetic linkage mapping and analysis of muscle fiber–related QTLs in common carp (Cyprinus carpio L.). Mar. Biotechnol. (NY) 13, 376–392 (2011).

Sun, X.W. & Liang, L.Q. A genetic linkage map of common carp (Cyprinus carpio L.) and mapping of a locus associated with cold tolerance. Aquaculture 238, 165–172 (2004).

Li, Y. et al. Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio. Mar. Biotechnol. (NY) 13, 706–712 (2011).

Xu, P. et al. Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. BMC Genomics 12, 188 (2011).

Christoffels, A., Bartfai, R., Srinivasan, H., Komen, H. & Orban, L. Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7 (suppl. 5), S2 (2006).

Zhang, Y. et al. Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. J. Integr. Bioinform. 8, 169 (2011).

Ji, P. et al. Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS ONE 7, e35152 (2012).

Williams, D.R. et al. Genomic resources and microarrays for the common carp Cyprinus carpio L. J. Fish Biol. 72, 2095–2117 (2008).

Henkel, C.V. et al. Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish 9, 59–67 (2012).

Ojima, Y. & Yamamoto, K. Cellular DNA contents of fishes determined by flow cytometry. La Kromosomo II 57, 1871–1888 (1990).

Kidwell, M.G. & Lisch, D.R. Transposable elements and host genome evolution. Trends Ecol. Evol. 15, 95–99 (2000).

Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002).

Van de Peer, Y. Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids. Genome Biol. 5, 250 (2004).

Kasahara, M. et al. The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714–719 (2007).

Jones, F.C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55–61 (2012).

Haas, B.J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).

Meyer, A. & Van de Peer, Y. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays 27, 937–945 (2005).

Hoegg, S., Brinkmann, H., Taylor, J.S. & Meyer, A. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J. Mol. Evol. 59, 190–203 (2004).

Santini, F., Harmon, L., Carnevale, G. & Alfaro, M. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol. Biol. 9, 194 (2009).

Crow, K.D. & Wagner, G.P. Proceedings of the SMBE Tri-National Young Investigators Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity? Mol. Biol. Evol. 23, 887–892 (2006).

Jaillon, O. et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946–957 (2004).

Zhang, Y. et al. Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family. J. Genet. Genomics 35, 97–103 (2008).

Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).

Amores, A. et al. Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714 (1998).

Mungpakdee, S. et al. Differential evolution of the 13 Atlantic salmon Hox clusters. Mol. Biol. Evol. 25, 1333–1343 (2008).

Davidson, W.S. et al. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 11, 403 (2010).

Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

Balon, E.K. Origin and domestication of the wild carp, Cyprinus carpio: from Roman gourmets to the swimming flowers. Aquaculture 129, 3–48 (1995).

Rohner, N. et al. Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication. Curr. Biol. 19, 1642–1647 (2009).

Millar, S.E. Molecular mechanisms regulating hair follicle development. J. Invest. Dermatol. 118, 216–225 (2002).

Hoekstra, H.E. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity 97, 222–234 (2006).

Ito, S. & Wakamatsu, K. Human hair melanins: what we have learned and have not learned from mouse coat color pigmentation. Pigment Cell Melanoma Res. 24, 63–74 (2011).

Miller, J.R. et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24, 2818–2824 (2008).

Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).

Neilan, B.A., Wilton, A.N. & Jacobs, D. A universal procedure for primer labelling of amplicons. Nucleic Acids Res. 25, 2938–2939 (1997).

Schuelke, M. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18, 233–234 (2000).

Sun, X. et al. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8, e58700 (2013).

Stanke, M., Schoffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).

Salamov, A.A. & Solovyev, V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516–522 (2000).

Campbell, M.A., Haas, B.J., Hamilton, J.P., Mount, S.M. & Buell, C.R. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7, 327 (2006).

Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48–D55 (2013).

Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

Zdobnov, E.M. & Apweiler, R. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001).

Ogata, H. et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29–34 (1999).

Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).

Li, L., Stoeckert, C.J. Jr. & Roos, D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).

Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).

Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. PHYML Online—a web server for fast maximum likelihood–based phylogenetic inference. Nucleic Acids Res. 33, W557–W559 (2005).

Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).

Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).

Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003).

Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739 (2011).

Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

Rosenberg, N.A. DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4, 137–138 (2004).

Vilella, A.J., Blanco-Garcia, A., Hutter, S. & Rozas, J. VariScan: analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21, 2791–2793 (2005).

Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

Li, B. & Dewey, C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).

Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).