Characterization of common carp transcriptome: Sequencing, de novo assembly, annotation and comparative genomics

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Ji, Peifeng ^a   Liu, Guiming ^b   Xu, Jian ^a   Wang, Xumin ^b   Li, Jiongtang ^a   Zhao, Zixia ^a   Zhang, Xiaofeng ^a   Zhang, Yan ^a   Xu, Peng ^a   Sun, Xiaowen ^a  

^a SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

^b Chinese Academy of Sciences and China National Center for Bioinformation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; TRANSCRIPTOME; MICROSATELLITE DNA;

ARTICLE; CARP; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA FLANKING REGION; FISH GENETICS; GENE CONTROL; GENE FUNCTION; GENE SEQUENCE; MICROSATELLITE MARKER; MOLECULAR GENETICS; NONHUMAN; OPEN READING FRAME; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; ZEBRA FISH; ANIMAL; EXPRESSED SEQUENCE TAG; GENETICS; GENOMICS; METHODOLOGY;

CYPRINIDAE; CYPRINUS CARPIO; DANIO RERIO; GASTEROSTEUS ACULEATUS; ORYZIINAE;

ANIMALS; CARPS; EXPRESSED SEQUENCE TAGS; GENOMICS; MICROSATELLITE REPEATS; OPEN READING FRAMES; TRANSCRIPTOME;

EID: 84859715310     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035152     Document Type: Article

References (41)

1. FAO (2007) The state of world fisheries and aquaculture 2006: FAO.
2. Wang C-h, Li S-f, (2004) Phylogenetic relationships of ornamental (koi) carp, Oujiang color carp and Long-fin carp revealed by mitochondrial DNA COII gene sequences and RAPD analysis. Aquaculture 231: 83-91.
3. Kongchum P, Palti Y, Hallerman EM, Hulata G, David L, (2010) SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio). Fish & Shellfish Immunology 29: 356-361.
4. Kulhanek SA, Leung B, Ricciardi A, (2011) Using ecological niche models to predict the abundance and impact of invasive species: application to the common carp. Ecological Applications 21: 203-213.
5. van Campenhout K, Bervoets L, Redeker ES, Blust R, (2009) A kinetic model for the relative contribution of waterborne and dietary cadmium and zinc in the common carp (Cyprinus carpio). Environmental Toxicology and Chemistry 28: 209-219.
6. Kroupova H, Prokes M, Macova S, Penaz M, Barus V, et al. (2010) Effect of nitrite on early-life stages of common carp (Cyprinus carpio L.). Environmental Toxicology and Chemistry 29: 535-540.
7. Liu D, Liu S, You C, Chen L, Liu Z, et al. (2010) Identification and Expression Analysis of Genes Involved in Early Ovary Development in Diploid Gynogenetic Hybrids of Red Crucian Carp × Common Carp. Marine Biotechnology 12: 186-194.
8. Zhang Y, Liang L, Jiang P, Li D, Lu C, et al. (2008) Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family. Journal of Genetics and Genomics 35: 97-103.
9. Zhang Y, Liang L, Jiang P, Li D, Lu C, et al. (2008) 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.
10. Wang D, Liao X, Cheng L, Yu X, Tong J, (2007) Development of novel EST-SSR markers in common carp by data mining from public EST sequences. Aquaculture 271: 558-574.
11. Zhou J, Wu Q, Wang Z, Ye Y, (2004) Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Genetika 40: 1389-1393.
12. Sun X, Liang L, (2004) A genetic linkage map of common carp (Cyprinus carpio L.) And mapping of a locus associated with cold tolerance. Aquaculture 238: 8.
13. Cheng L, Liu L, Yu X, Wang D, Tong J, (2010) A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Anim Genet 41: 191-198.
14. Xu P, Wang J, Wang J, Cui R, Li Y, et al. (2011) Generation of the first BAC-based physical map of the common carp genome. BMC Genomics 12: 537.
15. Xu J, Huang W, Zhong C, Luo D, Li S, et al. (2011) Defining Global Gene Expression Changes of the Hypothalamic-Pituitary-Gonadal Axis in Female sGnRH-Antisense Transgenic Common Carp (Cyprinus carpio). PLoS ONE 6: e21057.
16. Williams DR, Li W, Hughes MA, Gonzalez SF, Vernon C, et al. (2008) Genomic resources and microarrays for the common carp Cyprinus carpio L. Journal of Fish Biology 72: 2095-2117.
17. Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L, (2006) Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7: S2.
18. Yan X, Ding L, Li Y, Zhang X, Liang Y, et al. (2012) Identification and Profiling of MicroRNAs from Skeletal Muscle of the Common Carp. PLoS ONE 7: e30925.
19. Li Y, Xu P, Zhao Z, Wang J, Zhang Y, et al. (2011) 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.
20. Xu P, Li J, Li Y, Cui R, Wang J, et al. (2011) Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. BMC Genomics 12: 188.
21. Moens LN, van der Ven K, van Remortel P, Del-Favero J, de Coen WM, (2007) Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray. J Biochem Mol Toxicol 21: 299-311.
22. Wan Y, Zhang Y, Ji P, Li Y, Xu P, et al. (2011) Molecular characterization of CART, AgRP, and MC4R genes and their expression with fasting and re-feeding in common carp (Cyprinus carpio). Molecular Biology Reports pp. 1-9.
23. Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, et al. (2010) Genetic Linkage Mapping and Analysis of Muscle Fiber-Related QTLs in Common Carp (Cyprinus carpio L.). Marine Biotechnology pp. 1-17.
24. Mao RX, Liu FJ, Zhang XF, Zhang Y, Cao DC, et al. (2009) [Studies on quantitative trait loci related to activity of lactate dehydrogenase in common carp (Cyprinus carpio)]. Yi Chuan 31: 407-411.
25. Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, et al. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 11: R8.
26. Abernathy J, Xu P, Li P, Xu D-H, Kucuktas H, et al. (2007) Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis. BMC Genomics 8: 176.
27. Wang Q, Wang Y, Xu P, Liu Z, (2006) NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis. Molecular immunology 43: 1676-1686.
28. Nandi S, Peatman E, Xu P, Wang S, Li P, et al. (2007) Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus). Genetica 131: 81-90.
29. Sha Z, Xu P, Takano T, Liu H, Terhune J, et al. (2008) The warm temperature acclimation protein Wap65 as an immune response gene: Its duplicates are differentially regulated by temperature and bacterial infections. Molecular immunology.
30. Hale M, Xu P, Scardina J, Wheeler P, Thorgaard G, et al. (2011) Differential gene expression in male and female rainbow trout embryos prior to the onset of gross morphological differentiation of the gonads. BMC Genomics 12: 404.
31. Xu P, McIntyre L, Scardina J, Wheeler P, Thorgaard G, et al. (2011) Transcriptome Profiling of Embryonic Development Rate in Rainbow Trout Advanced Backcross Introgression Lines. Marine Biotechnology 13: 215-231.
32. Hampton M, Melvin RG, Kendall AH, Kirkpatrick BR, Peterson N, et al. (2011) Deep Sequencing the Transcriptome Reveals Seasonal Adaptive Mechanisms in a Hibernating Mammal. PLoS ONE 6: e27021.
33. Hou R, Bao Z, Wang S, Su H, Li Y, et al. (2011) Transcriptome Sequencing and de Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX. PLoS ONE 6: e21560.
34. Jung H, Lyons RE, Dinh H, Hurwood DA, McWilliam S, et al. (2011) Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): de Novo Assembly, Annotation and Marker Discovery. PLoS ONE 6: e27938.
35. He S, Mayden RL, Wang X, Wang W, Tang KL, et al. (2008) Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46: 818-829.
36. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159.
37. Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
38. Kumar S, Blaxter ML, (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11: 571.
39. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M, (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 35: W182-W185.
40. Min XJ, Butler G, Storms R, Tsang A, (2005) TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Res 33: W669-672.
41. Thurston MI, Field D, (2005) Msatfinder: detection and characterisation of microsatellites.