A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp.
By economic value, shrimp is currently the most important seafood commodity worldwide, and these animals are often the subject of scientific research in shrimp farming countries. High throughput methods, such as expressed sequence tags (ESTs), were originally developed to study human genomics, but they are now available for studying other important organisms, including shrimp. ESTs are short sequences generated by sequencing randomly selected cDNA clones from a cDNA library. This is currently the most efficient and powerful method for providing transcriptomic data for organisms with an uncharacterized genome. This review will summarize the sixteen major shrimp EST studies that have been conducted to date. In addition, we analyzed the EST data downloaded from NCBI dbEST for the four major penaeid shrimp species and constructed a database to host all of these EST data as well as our own analysis results. This database provides the shrimp aquaculture research community with an outline of the shrimp transcriptome as well as a tool for shrimp gene identification.
Leu
Jiann-Horng
JH
Center for Marine Bioenviroment and Biotechnology, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung, 20224 Taiwan, Republic of China.
Chen
Shu-Hwa
SH
Wang
Yu-Bin
YB
Chen
Yen-Chen
YC
Su
Sheng-Yao
SY
Lin
Chung-Yen
CY
Ho
Jan-Ming
JM
Lo
Chu-Fang
CF
D000818:Animals; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation / Q000235:genetics*; D007113:Immunity, Innate / Q000235:genetics*; D033561:Penaeidae / Q000235:genetics*; D012098:Reproduction / Q000235:genetics; D019849:Sex Determination Processes / Q000235:genetics; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
Nat Genet. 1993 Jul;4(3):256-67
8358434
Arch Virol. 2002 Sep;147(9):1799-812
12209318
Dev Comp Immunol. 2005;29(8):681-91
15854680
Dev Comp Immunol. 2001 Sep;25(7):565-77
11472779
Mar Biotechnol (NY). 2006 Sep-Oct;8(5):491-500
16794954
Science. 2002 Apr 5;296(5565):141-5
11910074
Comp Biochem Physiol A Mol Integr Physiol. 2009 Jan;152(1):66-76
18824117
Mar Biotechnol (NY). 2002 Oct;4(5):487-94
14961242
Dis Aquat Organ. 2007 Mar 13;74(3):179-89
17465303
Fish Shellfish Immunol. 2007 Aug;23(2):459-72
17337210
Comp Biochem Physiol B. 1993 Jan;104(1):69-73
8448995
Methods Enzymol. 2005;395:400-18
15984049
Dev Comp Immunol. 2005;29(2):103-12
15450750
FEBS Lett. 2000 Sep 29;482(1-2):13-8
11018515
Comp Biochem Physiol A Mol Integr Physiol. 2006 Feb;143(2):155-61
16406641
Bioinformatics. 2003 Mar 22;19(5):651-2
12651724
Nucleic Acids Res. 2008 Jan;36(Database issue):D190-5
18045787
Mar Biotechnol (NY). 1999 Sep;1(5):465-0476
10525681
Dis Aquat Organ. 2004 Oct 21;61(1-2):123-35
15584419
Curr Opin Immunol. 2002 Feb;14(1):87-95
11790537
Plant Mol Biol. 2006 Jan;60(1):69-85
16463100
Fish Shellfish Immunol. 2002 Jul;13(1):69-83
12201653
J Biochem Mol Biol. 2007 Jul 31;40(4):501-10
17669265
Arch Virol. 2003 Dec;148(12):2381-96
14648293
Physiol Genomics. 2007 Mar 14;29(1):44-56
17148689
Nucleic Acids Res. 2001 Jan 1;29(1):159-64
11125077
Genome Res. 2004 Oct;14(10B):2121-7
15489334
Biochem Biophys Res Commun. 1991 Jun 28;177(3):1306-12
1905538
Fish Shellfish Immunol. 2008 Nov;25(5):485-93
18692576
Genome Res. 2003 Jun;13(6B):1273-89
12819125
Fish Shellfish Immunol. 2008 Jan;24(1):46-54
18083045
BMC Genomics. 2007 May 16;8:120
17506900
Integr Comp Biol. 2006 Dec;46(6):931-9
21672797
Science. 1987 Jan 9;235(4785):202-5
17778635
Science. 1991 Jun 21;252(5013):1651-6
2047873
Cell Signal. 1993 Jan;5(1):69-80
8452755
Fish Shellfish Immunol. 2003 Jul;15(1):71-90
12833917
Gene. 2006 Dec 15;384:104-12
16945489
Development. 2002 Oct;129(20):4739-51
12361966
Genome Res. 1999 Sep;9(9):868-77
10508846
Brief Bioinform. 2000 Feb;1(1):76-92
11466975
Antiviral Res. 2005 Apr;66(1):39-45
15781131
Trends Plant Sci. 2003 Jul;8(7):321-9
12878016