Analysis of the Skin Transcriptome in Two Oujiang Color Varieties of Common Carp

Background Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding. Methodology/Principal Findings In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW. Conclusions The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.

[1]  E. Balon.  Origin and domestication of the wild carp, Cyprinus carpio: from Roman gourmets to the swimming flowers , 1995 .

[2]  Stephen L. Johnson,et al.  The evolution of morphological complexity in zebrafish stripes. , 2002, Trends in genetics : TIG.

[3]  Terri K. Attwood,et al.  PRINTS and PRINTS-S shed light on protein ancestry , 2002, Nucleic Acids Res..

[4]  J. Volff,et al.  Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. , 2002, Genetics.

[5]  M. Feldman,et al.  Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. , 2003, Molecular biology and evolution.

[6]  Agricultural development and the opportunities for aquatic resources research in China , 2003 .

[7]  N. Okada,et al.  The evolution of genes for pigmentation in African cichlid fishes. , 2004, Gene.

[8]  L. David,et al.  Aspects of red and black color inheritance in the Japanese ornamental (Koi) carp (Cyprinus carpio L.) , 2004 .

[9]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[10]  E. Liu,et al.  Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation , 2005, Nature Methods.

[11]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[12]  Eric H Davidson,et al.  The Transcriptome of the Sea Urchin Embryo , 2006, Science.

[13]  Manfred Schartl,et al.  Evolution of pigment synthesis pathways by gene and genome duplication in fish , 2007, BMC Evolutionary Biology.

[14]  I. Jackson,et al.  Regulation of pigmentation in zebrafish melanophores. , 2006, Pigment cell research.

[15]  P. Insel,et al.  A Single Amino Acid Mutation Contributes to Adaptive Beach Mouse Color Pattern , 2006, Science.

[16]  J. T. Bagnara,et al.  On the blue coloration of vertebrates. , 2007, Pigment cell research.

[17]  H. Hoekstra,et al.  Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes , 2007, PLoS Biology.

[18]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[19]  He Xiao-zhen.  Preliminary study on inheritance of red and white color phenotypes in Oujiang color carp,C.carpio var.color , 2008 .

[20]  I. Jackson,et al.  mc1r Pathway regulation of zebrafish melanosome dispersion. , 2008, Zebrafish.

[21]  Meredith E. Protas,et al.  Evolution of coloration patterns. , 2008, Annual review of cell and developmental biology.

[22]  J. Volff,et al.  Pigmentary function and evolution of tyrp1 gene duplicates in fish , 2009, Pigment cell & melanoma research.

[23]  J. Volff,et al.  Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish , 2009, Genome biology and evolution.

[24]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[25]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[26]  Amos Bairoch,et al.  PROSITE, a protein domain database for functional characterization and annotation , 2009, Nucleic Acids Res..

[27]  Sébastien Renaut,et al.  Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae) , 2010, Molecular ecology.

[28]  L. Morrell,et al.  Colour change and assortment in the western rainbowfish , 2010, Animal Behaviour.

[29]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[30]  T. Visser,et al.  Transcriptional profiling of fibroblasts from patients with mutations in MCT8 and comparative analysis with the human brain transcriptome , 2010, Human molecular genetics.

[31]  Songnian Hu,et al.  Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection , 2010, BMC Genomics.

[32]  J. Yao,et al.  Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches , 2010, BMC Genomics.

[33]  Z. Nagy,et al.  Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequence , 2010 .

[34]  Chenghui Wang,et al.  Genetic differentiation of wild and hatchery Oujiang color common carp: potential application to the identification of escapees , 2011, Fisheries Science.

[35]  Hongxia Wang,et al.  Transcriptomic Analysis of the Clam Meretrix meretrix on Different Larval Stages , 2011, Marine Biotechnology.

[36]  Susan C. Jones,et al.  Transcriptomics of the Bed Bug (Cimex lectularius) , 2011, PloS one.

[37]  Wenjia Yang,et al.  Transcriptome Analysis of the Oriental Fruit Fly (Bactrocera dorsalis) , 2011, PloS one.

[38]  Shane C. Burgess,et al.  Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines , 2012, PloS one.

[39]  G. Qiu,et al.  Transcriptome Analysis of the Oriental River Prawn, Macrobrachium nipponense Using 454 Pyrosequencing for Discovery of Genes and Markers , 2012, PloS one.

[40]  J. Pérez‐Sánchez,et al.  Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts , 2013, BMC Genomics.

[41]  Shuhong Zhao,et al.  Identification of Genes Related to White and Black Plumage Formation by RNA-Seq from White and Black Feather Bulbs in Ducks , 2012, PloS one.

[42]  J. Yao,et al.  RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout , 2012, PloS one.

[43]  Guiming Liu,et al.  Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics , 2012, PloS one.

[44]  C. Li,et al.  High Throughput Mining and Characterization of Microsatellites from Common Carp Genome , 2012, International journal of molecular sciences.

[45]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[46]  Panwen Wang,et al.  A fast and accurate SNP detection algorithm for next-generation sequencing data , 2012, Nature Communications.

[47]  Zhanjiang Liu,et al.  RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. , 2012, Fish & shellfish immunology.

[48]  A. Figueras,et al.  High-Throughput Sequence Analysis of Turbot (Scophthalmus maximus) Transcriptome Using 454-Pyrosequencing for the Discovery of Antiviral Immune Genes , 2012, PloS one.

[49]  Songlin Chen,et al.  Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species , 2013, PloS one.

[50]  Zhuo Li-yan.  Observation and analysis of growth dynamics in Oujiang color common carp with different pigmentation types , 2013 .

[51]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.