Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Che, Rongbo ^a   Sun, Yueyan ^a   Sun, Dianqiao ^a   Xu, Tianjun ^a  

^a ZHEJIANG OCEAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; FISH; FISH GENETICS; GENE IDENTIFICATION; IMMUNITY; KIDNEY; LIVER; MIIUY CROAKER; NONHUMAN; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SPLEEN; ANIMAL; GENETIC DATABASE; GENETICS; METABOLISM; PERCIFORMES;

ANIMALS; DATABASES, GENETIC; KIDNEY; LIVER; PERCIFORMES; SPLEEN; TRANSCRIPTOME;

EID: 84899551948     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094046     Document Type: Article

References (56)

1. Froese R, Pauly D (2012) FishBase:World Wide Web electronic publication. http://www.fishbase.org.
2. Lou B (2004) Biology and breeding technology of Miichthys miiuy. Chin J Mod Fish 6:11-13.
3. Shan XJ, Dou SZ (2009) Allometric growth of croaker (Miichthys miiuy) larvae and juveniles and its ecological implication. Oceanologia et Limnologia Sinica 40:714-718.
4. Shan LZ, Xie QL, Shao XB, Yan MC (2010) Study on embryonic development and morphological characteristic habitual behavior for larvae, juvenile and young of Miichthys Miiuy. China Mar Sci 34:75-80.
5. Bondad-Reantaso MG (2007) Assessment of freshwater fish seed resources for sustainable aquaculture. Rome: Food and Agriculture Organization of the United Nations.
6. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W (2000) Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev 64:655-671. (Pubitemid 32475925)
7. Grisez L, Tan Z (2005) Vaccine development for Asian Aquaculture. In Diseases in Asian Aquaculture V Fish health section, Proceedings of the Fifth Symposium in Asian Aquaculture Edited by: Walker P, Lester R, Bondad-Reantaso MG. Goldcoast, Australia: Asian Fisheries Society 483-494.
8. Dumetz F, Duchaud E, LaPatra SE, Marrec CL, Claverol S, et al. (2006) A protective immune response is generated in rainbow trout by an OmpH-Like surface antigen (P18) of Flavobacterium psychrophilum. Appl Environ Microbiol 72:4845-4852. (Pubitemid 44078812)
9. Cheng YZ, Wang RX, Sun YN, Xu TJ (2011) Molecular characterization of miiuy croaker CC chemokine gene and its expression following Vibrio anguillarum injection. Fish Shellfish Immunol 31:148-154.
10. Xu TJ, Cheng YZ, Shi G, Wang RX (2011) Molecular cloning, characterization, and expression analysis of a disease-resistance related CC chemokine gene in miiuy croaker (Miichthys miiuy). Aquaculture 318:25-32.
11. Cheng YZ, Wang RX, Xu TJ (2011) Molecular cloning, characterization and expression analysis of a miiuy croaker (Miichthys miiuy) CXC chemokine gene resembling the CXCL9/CXCL10/CXCL11. Fish Shellfish Immunol 31:439-445.
12. Meng FX, Wang RX, Xu TJ, Sun YN, Cheng YZ, et al. (2012) An unexpected loss of domains in the conservative evolution ninth complement component in a higher teleost, Miichthys miiuy. Fish Shellfish Immunol 32:1171-1178.
13. Xu TJ, Sun YN, Cheng YZ, Shi G, Wang RX (2011) Genomic sequences comparison and differential expression of miiuy croaker MHC class I gene, after infection by Vibrio anguillarum. Dev Comp Immunol 35:483-489.
14. Xu TJ, Sun YN, Shi G, Cheng YZ, Wang RX (2011) Characterization of the major histocompatibility complex class II genes in miiuy croaker. PLoS One 6:e23823.
15. Xu TJ, Sun YN, Shi G, Wang RX (2012) Miiuy Croaker Hepcidin Gene and Comparative Analyses Reveal Evidence for Positive Selection. PLoS One 7:e35449.
16. Sun YN, Xu TJ, Wang JX, Cheng YZ, Wang RX (2011) Sequence and expression analysis of cathepsin S gene in the miiuy croaker Miichthys miiuy. Fish Physiol Biochem 37:761-765.
17. Liu XZ, Shi G, Cui DL, Wang RX, Xu TJ (2012) Molecular cloning and comprehensive characterization of cathepsin D in the Miiuy croaker Miichthys miiuy. Fish Shellfish Immunol 32:464-468.
18. Xu TJ, Meng FX, Sun YN, Shi G, Wang RX (2010) Identification of immune genes of the miiuy croaker (Miichthys miiuy) by sequencing and bioinformatic analysis of ESTs. Fish Shellfish Immunol 29:1099-1105.
19. Wang RX, Xu TJ, Sun YN, He GY (2010) Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae). Genet Mol Res 9:931-934.
20. Xu TJ, Sun DQ, Sun YN, Wang RX (2011) Development of 30 novel polymorphic expressed sequence tags (EST)-derived microsatellite markers for the miiuy croaker, Miichthys miiuy. Int J Mol Sci 12:4021-4026.
21. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349. (Pubitemid 351929471)
22. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 7:334-346.
23. Hegedus Z, Zakrzewska A, Agoston VC, Ordas A, Racz P, et al. (2009) Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol 46:2918-2930.
24. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res 20:413-427.
25. Jacob NM, Kantardjieff A, Yusufi FN, Retzel EF, Mulukutla BC, et al. (2010) Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol Bioeng 105:1002-1009.
26. Wang B, Guo G, Wang C, Lin Y, Wang X, et al. (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38:5075-5087.
27. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
28. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456:60-65.
29. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10:219.
30. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265-272.
31. Xiang LX, He D, Dong WR, Zhang YW, Shao JZ. (2010) Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immunerelevant genes in marine fish. BMC Genomics 11:472.
32. Morais S, Pratoomyot J, Taggart JB, Bron JE, Guy DR, et al. (2011) Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis. BMC Genomics 12:255.
33. Xia JH, Yue GH (2010) Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer. BMC Genomics 11:356.
34. Salem M, Rexroad III CE, Wang JN, Thorgaard GH, Yao JB (2010) Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11:564.
35. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180.
36. Hou R, Bao ZM, Wang S, Su HL, Li Y, et al. (2011) Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX. PLoS One 6(6):e21560.
37. Bai XD, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O (2011) Transcriptomics of the Bed Bug (Cimex lectularius). PLoS One 6:e16336.
38. Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA (2011) Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 12:370.
39. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS. de novo assembly of whole-genome shotgun microreads. Genome Res 18:810-820. (Pubitemid 351645071)
40. Miller HC, Biggs PJ, Voelckel C, Nelson NJ (2012) De novo sequence assembly and characterization of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics 13:439.
41. Li RQ, Zhu HM, Ruan J, Qian W, Fang XD, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265-272.
42. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-714. (Pubitemid 351321217)
43. Wang Z, Fang B, Chen J, Zhang X, Luo Z, et al. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11:726.
44. Wang XJ, Xu RH, Wang RL, Liu AZ (2012) Transcriptome analysis of Sacha Inchi (Plukenetia volubilis L.) seeds at two developmental stages. BMC Genomics 13:716.
45. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 7:138-148.
46. Li DJ, Deng Z, Qin B, Liu XH, Men ZH (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192.
47. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676. (Pubitemid 41264107)
48. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue): W293-297.
49. Peng Y, Abercrombie LLG, Yuan JS, Riggins CW, Sammons RD, et al. (2010) Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes. Pest Manage Sci 66:1053-1062.
50. Lin AF, Xiang LX, Wang QL, Dong WR, Gong YF, et al. (2009) The DC-SIGN of zebrafish: insights into the existence of a CD209 homologue in a lower vertebrate and its involvement in adaptive immunity. J Immunol 183:7398-7410.
51. Gong YF, Xiang LX, Shao JZ (2009) CD154-CD40 interactions are essential for thymus-dependent antibody production in zebrafish: insights into the origin of costimulatory pathway in helper T cell-regulated adaptive immunity in early vertebrates. J Immunol 182:7749-7762.
52. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-86.
53. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422. (Pubitemid 36599853)
54. Li R, Li Y, Fang X, Yang H, Wang J, et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124-1132.
55. Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg J Bot 129:157.
56. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295. (Pubitemid 43373825)