Generation and Analysis of 10,443 ESTs from Cephalothorax of Fenneropenaeus Chinensis

Chinese shrimp, Fenneropenaeus chinensis (F. chinensis), is one of the main local mariculture species in China. To accelerate gene discovery, facilitate genetic mapping and develop marker-assisted selection, a total of 10,446 expressed sequence tags (ESTs) were created from the 5' ends of randomly selected clones from a cephalothorax cDNA library of an adult female F. chinensis. The ESTs were clustered into 1399 contigs and 1720 singletons; represent about 3120 unique genes discovered. Among the discovered unique genes, 1373 EST clusters are known genes and 1747 EST clusters may represent novel genes, which do not match any known genes from other species. Known ESTs in the dataset were classified in to different molecular-function categories according to the KEGG-GO and the enzyme was the biggest category, which consist of 29.5% of known ESTs. The putative novel genes were characterized by motif search, and the functions of about 50% (786) of these genes were preliminarily determined. Among them, type I antifreeze protein was considered as the most redundant one. Besides the discovery of new genes through EST analysis, 324 (about 3%) perfect simple sequence repeats (SSRs) were found. This EST approach provides a foundation for the discovery of functional genes and furthermore gives great support for future microarray studies on gene expression.

[1]  L. Ingram,et al.  Sucrose and overexpression of trehalose biosynthetic genes (otsBA) increase desiccation tolerance of recombinant Escherichia coli , 2008, Biotechnology Letters.

[2]  M. Foti,et al.  Human Immunodeficiency Virus Type 1 and Influenza Virus Exit via Different Membrane Microdomains , 2007, Journal of Virology.

[3]  S. Klinbunga,et al.  Expressed sequence tag analysis for identification and characterization of sex-related genes in the giant tiger shrimp Penaeus monodon. , 2007, Journal of biochemistry and molecular biology.

[4]  Q. Sattentau,et al.  Human Immunodeficiency Virus Type 1 Assembly, Budding, and Cell-Cell Spread in T Cells Take Place in Tetraspanin-Enriched Plasma Membrane Domains , 2007, Journal of Virology.

[5]  Chun-Wei Hsu,et al.  Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon , 2007, BMC Genomics.

[6]  J. Xiang,et al.  Microsatellite-centromere distances and microsatellite diversity in different ploidy classes of Chinese shrimp (Fenneropenaeus Chinensis) , 2007, Genetica.

[7]  K. Miyamoto,et al.  Spindles of an Entomopoxvirus Facilitate Its Infection of the Host Insect by Disrupting the Peritrophic Membrane , 2007, Journal of Virology.

[8]  C. Lursinsap,et al.  Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database. , 2006, Gene.

[9]  Bing Wang,et al.  Discovery of the Genes in Response to White Spot Syndrome Virus (WSSV) Infection in Fenneropenaeus chinensis Through cDNA Microarray , 2006, Marine Biotechnology.

[10]  N. O'Leary,et al.  Analysis of multiple tissue-specific cDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei. , 2006, Integrative and comparative biology.

[11]  Xiao-Fan Zhao,et al.  Identification and molecular characterization of a peritrophin-like protein from fleshy prawn (Fenneropenaeus chinensis). , 2006, Molecular immunology.

[12]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[13]  I. Coulibaly,et al.  Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss) , 2005, BMC Genomics.

[14]  V. Gahtan,et al.  The role of thrombospondin-1 in human disease. , 2004, The Journal of surgical research.

[15]  Rath Pichyangkura,et al.  Antimicrobial peptides discovered in the black tiger shrimp Penaeus monodon using the EST approach. , 2004, Diseases of aquatic organisms.

[16]  Lei Liu,et al.  Multi-species comparative mapping in silico using the COMPASS strategy , 2004, Bioinform..

[17]  K. Klimpel,et al.  Identification of differentially expressed genes in shrimp (Penaeus stylirostris) infected with White spot syndrome virus by cDNA microarrays , 2003, Archives of Virology.

[18]  R. Bhatnagar,et al.  Synthetic propeptide inhibits mosquito midgut chitinase and blocks sporogonic development of malaria parasite. , 2003, Biochemical and biophysical research communications.

[19]  Rolf Apweiler,et al.  Applications of InterPro in Protein Annotation and Genome Analysis , 2002, Briefings Bioinform..

[20]  P. Friedl,et al.  The role of thrombospondin-1 in apoptosis , 2002, Cellular and Molecular Life Sciences CMLS.

[21]  Joseph White,et al.  Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index , 2002, Mammalian Genome.

[22]  J. Silva.  Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs) , 2001 .

[23]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[24]  M. Jacobs-Lorena,et al.  The peritrophic matrix of hematophagous insects. , 2001, Archives of insect biochemistry and physiology.

[25]  G. L. Bennett,et al.  Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. , 2001, Genome research.

[26]  R. Tellam,et al.  Chitin is only a minor component of the peritrophic matrix from larvae of Lucilia cuprina. , 2000, Insect biochemistry and molecular biology.

[27]  C. Soderlund,et al.  Contigs built with fingerprints, markers, and FPC V4.7. , 2000, Genome research.

[28]  R. J. Henry,et al.  Analysis of SSRs derived from grape ESTs , 2000, Theoretical and Applied Genetics.

[29]  T. Hirokawa,et al.  Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. , 1999, Biophysical chemistry.

[30]  Zhanjiang Liu,et al.  Development of Polymorphic EST Markers Suitable for Genetic Linkage Mapping of Catfish , 1999, Marine Biotechnology.

[31]  A. Triplett,et al.  A peritrophin-like protein expressed in the embryonic tracheae of Drosophila melanogaster. , 1999, Insect biochemistry and molecular biology.

[32]  Zhicheng Shen,et al.  A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin. Cloning, expression, and characterization. , 1998, The Journal of biological chemistry.

[33]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[34]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[35]  M. Kanehisa.  A database for post-genome analysis. , 1997, Trends in genetics : TIG.

[36]  I. East,et al.  Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a mammalian host. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[37]  J. Lahav.  The functions of thrombospondin and its involvement in physiology and pathophysiology. , 1993, Biochimica et biophysica acta.

[38]  P. Bornstein,et al.  Thrombospondins: structure and regulation of expression , 1992, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[39]  J. Clegg,et al.  Aerobic heat shock activates trehalose synthesis in embryos of Artemia franciscana , 1992, FEBS letters.

[40]  J. Craig Venter,et al.  Sequence identification of 2,375 human brain genes , 1992, Nature.

[41]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[42]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[43]  Rodger Staden,et al.  Software for genome mapping by fingerprinting techniques , 1988, Comput. Appl. Biosci..

[44]  A. Boulesteix,et al.  Functional genomics: tools for improving farm animal health and welfare. , 2005, Revue scientifique et technique.

[45]  W. Tong,et al.  Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs , 2004 .

[46]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[47]  Zhou Ling.  Isolation of microsatellite markers from Fenneropenaeus chinensis ESTs , 2003 .

[48]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[49]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[50]  M. Lehane.  Peritrophic matrix structure and function. , 1997, Annual review of entomology.

[51]  Lehane Mj.  Peritrophic matrix structure and function. , 1997 .

[52]  P. Sandifer,et al.  Meiotic Chromosome Complements and Nuclear Dna Contents of Four Species of Shrimps of the Genus Penaeus , 1990 .