Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers

Molecular Ecology Resources

Volumn 14, Issue 1, 2014, Pages 127-138

  Zhou, Z C ^a   Dong, Y ^a   Sun, H J ^a   Yang, A F ^a   Chen, Z ^a   Gao, S ^a   Jiang, J W ^a   Guan, X Y ^a   Jiang, B ^a   Wang, B ^a  

^a LIAONING OCEAN AND FISHERIES SCIENCE RESEARCH INSTITUTE   (China)

Author keywords

Markers development; Sea cucumber (Apostichopus japonicus); Transcriptome sequencing

Indexed keywords

APOSTICHOPUS JAPONICUS; HOLOTHUROIDEA;

LIPOPOLYSACCHARIDE; MICROSATELLITE DNA; TRANSCRIPTOME;

ANIMAL; ARTICLE; BIOLOGY; DRUG EFFECT; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; MARKERS DEVELOPMENT; MOLECULAR GENETICS; PHYSIOLOGICAL STRESS; SEA CUCUMBER; SEA CUCUMBER (APOSTICHOPUS JAPONICUS); SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHEAST ASIA; TRANSCRIPTOME SEQUENCING;

MARKERS DEVELOPMENT; SEA CUCUMBER (APOSTICHOPUS JAPONICUS); TRANSCRIPTOME SEQUENCING;

ANIMALS; ASIA, SOUTHEASTERN; COMPUTATIONAL BIOLOGY; GENETIC MARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIPOPOLYSACCHARIDES; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEA CUCUMBERS; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

EID: 84890236258     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12147     Document Type: Article

References (66)

1. Aparicio G, Gotz S, Conesa A et al. (2006) Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis. Studies in Health Technology and Informatics, 120, 194-204.
2. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Research, 7, 986-995.
3. Bejerano G, Pheasant M, Makunin I et al. (2004) Ultraconserved elements in the human genome. Science, 304, 1321-1325.
4. Benjamini Y, Drai D, Elmer G et al. (2001) Controlling the false discovery rate in behavior genetics research. Behavioural Brain Research, 125, 279-284.
5. Calduch-Giner JA, Bermejo-Nogales A, Benedito-Palos L et al. (2013) Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts. BMC Genomics, 14, 178.
6. Carroll RL (1997) Patterns and Processes of Vertebrate Evolution. Cambridge University Press, New York.
7. Castoe TA, Gu W, de Koning AP et al. (2009) Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research, 127, 112-127.
8. Chen S, Yang PC, Jiang F et al. (2010) De Novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS ONE, 5, e15633.
9. Clark MS, Thorne MAS, Vieira FA et al. (2010) Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics, 11, 362.
10. Defaveri J, Viitaniemi H, Leder E et al. (2013) Characterization genic and nongenic molecular markers: comparison of microsatellites and SNPs. Molecular Ecology Resources, 13, 377-392.
11. Dermitzakis ET, Kirkness E, Schwarz S et al. (2004) Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Research, 14, 852-859.
12. Du HX, Bao ZM, Hou R et al. (2012) Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867). PLoS ONE, 7, e33311.
13. Eeckhaut I, Parmentier E, Becker P et al. (2004) Parasites and biotic diseases in field and cultivated sea cucumbers. Advances in Sea Cucumber Aquaculture and Management, 463, 311-325.
14. Ellegren H (2008) Comparative genomics and the study of evolution by natural selection. Molecular Ecology, 17, 4586-4596.
15. Franchini P, Merwe M, Roodt-Wilding R (2011) Transcriptome characterizationof the South African abalone Haliotis midae using sequencing-by-synthesis. BMC Research Notes, 4, 59.
16. Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources, 10, 915-934.
17. Geraldes A, Difazio SP, Slavov GT et al. (2013) A 34 K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources, 13, 306-323.
18. Grabherr MG, Haas BJ, Yassour M et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
19. Guindon S, Gascuel O (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
20. Guindon S, Dufayard JF, Lefort V et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307-321.
21. Hou R, Bao ZM, Wang S et al. (2011) Transcriptome sequencing and De Novo analysis for Yesso Scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS ONE, 6, e21560.
22. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceeding of the Seventh International Conference on Intelligent Systems for Molecular Biology, 7, 138-148.
23. Kang JH, Kim YK, Kim MJ et al. (2011) Genetic differentiation among populations and color variants of sea cu-cumbers (Stichopus Japonicus) from Korea and China. International Journal of Biological Sciences, 7, 323-332.
24. Kircher M, Heyn P, Kelso J (2011) Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12, 382.
25. Kocot KM, Cannon JT, Todt C et al. (2011) Phylogenomics reveals deep molluscan relationships. Nature, 477, 452-456.
26. Kryukov GV, Schmidt S, Sunyaev S (2005) Small fitness effect of mutation in highly conserved non-coding regions. Human Molecular Genetics, 14, 2221-2229.
27. Li H, Coghlan A, Ruan J et al. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Research, 34, D572-D580.
28. Li Q, Chen L, Kong LF (2009a) A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers. Animal Genetics, 40, 678-685.
29. Li RQ, Li YR, Fang XD et al. (2009b) SNP detection for massively parallel whole-genome resequencing. Genome Research, 19, 1124-1132.
30. Liu SK, Zhou ZC, Lu JG et al. (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics, 12, 53.
31. Lynch M, Koskella B, Schaack S (2006) Mutation pressure and the evolution of organelle genomic architecture. Science, 311, 1727-1730.
32. Malone JH, Oliver B (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biology, 9, 34.
33. Meusemann K, von Reumont BM, Simon S et al. (2010) A phylogenomic approach to resolve the arthropod tree of life. Molecular Biology and Evolution, 27, 2451-2464.
34. Meyer E, Aglyamova GV, Wang S et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics, 10, 219.
35. Morin PA, Luikart G, Wayne RK et al. (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208-216.
36. Mortazavi A, Williams BA, McCue K et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621-628.
37. Nagalakshmi U, Waern K, Snyder M (2010) RNA-seq: a method for comprehensive transcriptome analysis. Current Protocols in Molecular Biology, 4, 1-13.
38. Nelson RJ, Cooper G, Garner T et al. (2002) Polymorphic markers for the sea cucumber Parastichopus californicus. Molecular Ecology Notes, 2, 233-235.
39. Novaes E, Drost DR, Farmerie WG et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9, 312.
40. Peng W, Bao ZM, Du HX et al. (2009) Development and characterization of 38 novel EST-SSRs for the sea cucumber Apostichopus japonicus. Conservation Genetics Resources, 1, 447-450.
41. Peng W, Bao ZM, Du HX et al. (2012) Development and characterization of 70 novel microsatellite markers for the sea cucumber (Apostichopus japonicus). Genetics and Molecular Research, 11, 434-439.
42. Pertea G, Huang XQ, Liang F et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19, 651-652.
43. Qin J, Huang Z, Chen J et al. (2012) Sequencing and de novo analysis of Crassostrea angulata (Fujian oyster) from 8 different developing phases using 454 GSFlx. PLoS ONE, 7, e43653.
44. Ramírez-Gómez F, Ortíz-Pineda PA, Rojas-Cartagena C et al. (2008) Immune-related genes associated with intestinal tissue in the sea cucumber Holothuria glaberrima. Immunogenetics, 60, 57-71.
45. Ramírez-Gómez F, Ortiz-Pineda PA, Rivera-Cardona G et al. (2009) LPS-induced genes in intestinal tissue of the sea cucumber Holothuria glaberrima. PLoS ONE, 4, e6178.
46. Roberts SB, Hauser L, Seeb LW et al. (2012) Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing. PLoS ONE, 7, e30908.
47. Russell J, Booth A, Fuller J et al. (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome, 47, 389-398.
48. Santiago P, Roig-Lopez JL, Santiago C et al. (2000) Serum amyloid a protein in an echinoderm: its primary structure and expression during intestinal regeneration in the sea cucumber Holothuria glaberrima. Journal of Experimental Zoology, 288, 335-344.
49. Santiago-Cardona PG, Berrios CA, Ramirez F et al. (2003) Lipopolysaccharides induce intestinal serum amyloid A expression in the sea cucumber Holothuria glaberrima. Developmental and Comparative Immunology, 27, 105-110.
50. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1135-1145.
51. Sun WJ, Li Q, Kong LF (2010) Characterization of thirteen single nucleotide polymorphism markers in the sea cucumber (Apostichopus japonicus). Conservation Genetics Resources, 2, 141-144.
52. Sun LN, Chen MY, Yang HS et al. (2011) Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus. Comparative Biochemistry and Physiology, 6, 95-205.
53. Surget-Groba Y, Montoya-Burgos JI (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Research, 20, 1432-1440.
54. Vera M, Alvarez-Dios JA, Fernandez C et al. (2013) Development and validation of single nucleotide polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) using high-throughput genotyping. International Journal of Molecular Sciences, 14, 5694-5711.
55. Vigerust DJ, Vick S, Shepherd VL (2012) Characterization of functional mannose receptor in a continuous hybridoma cell line. BMC Immunology, 13, 51.
56. Wang ET, Sandberg R, Luo S et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
57. Xu J, Ji P, Zhao Z et al. (2012) Genome-wide SNP discovery from transcriptome of four common carp strains. PLoS ONE, 7, e48140.
58. Yang AF, Zhou ZC, He CB et al. (2009) Analysis of expressed sequence tags from body wall, intestine and respiratory tree of sea cucumber (Apostichopus japonicus). Aquaculture, 296, 193-199.
59. Yang AF, Zhou ZC, Dong Y et al. (2010) Expression of immune-related genes in embryos and larvae of sea cucumber Apostichopus japonicus. Fish and Shellfish Immunology, 29, 839-845.
60. Yang AF, Sun DP, Liu SK et al. (2012) Characterization of fifteen SNP markers by mining EST in sea cucumber, Apostichopus japonicus. Journal of Genetics, 91, 49-53.
61. Yu XJ, Zheng HK, Wang J et al. (2006) Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. Genomics, 88, 745-751.
62. Zakas C, Schult N, McHugh D et al. (2012) Transcriptome analysis and SNP development can resolve population differentiation of Streblospio benedicti, a developmentally dimorphic marine annelid. PLoS ONE, 7, e31613.
63. Zhan AB, Bao ZM, Lu W et al. (2007) Development and characterization of 45 novel microsatellite markers for sea cucumber (Apostichopus japonicus). Molecular Ecology Notes, 7, 1345-1348.
64. Zheng FX, Sun XQ, Fang BH et al. (2006) Comparative analysis of genes expressed in regenerating intestine and non-eviscerated intestine of Apostichopus japonicus Selenka (Aspidochirotida: Stichopodidae) and cloning of ependymin gene. Hydrobiologia, 571, 109-122.
65. Zhou ZC, Sun DP, Yang AF et al. (2011) Molecular characterization and expression analysis of a complement component 3 in the sea cucumber (Apostichopus japonicus). Fish and Shellfish Immunology, 31, 540-547.
66. Zhu C, Cheng L, Tong J et al. (2012) Development and characterization of new single nucleotide polymorphism markers from expressed sequence tags in common carp (Cyprinus carpio). International Journal of Molecular Sciences, 13, 7343-7353.