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Analysis of expressed sequence tags from abdominal muscle cDNA library of the pacific white shrimp Litopenaeus vannamei

Published online by Cambridge University Press:  01 September 2008

J. R. Cesar ,
B. Zhao  and
J. Yang
J. R. Cesar
Affiliation:
Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
B. Zhao
Affiliation:
Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
J. Yang*
Affiliation:
Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
*
E-mail: Jinzeng@hawaii.edu
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Abstract

The pacific white shrimp, Litopenaeus vannamei, is a popular species in aquaculture. Abdominal muscle accounts for 90% of shrimp flesh. Its growth and related genes, particularly the regulatory genes, is not well known. A cDNA library of shrimp juvenile abdominal muscle was established by PCR-based SMART™ cDNA technology. Library size was 5.0 × 106 pfu (plaque-forming unit) independent clones per microgram of starting RNA with the percentage of recombinant clones >95%. Sequence analysis of 311 randomly picked positive clones revealed 197 expressed sequence tags with average insert size of 745 nucleotides, 56% (110 of 197) clones having 5′-end sequence and 44% (87 of 197) clones having 3′-end sequence. Queries of the sequences by Blast identified 37 unknown sequences, and 160 unique clones, including 67 sequences of 100% identity matches, 28 high homologies (80% to 90% sequence match, >100 bits hit score in Blastn), 65 medium homologies (>100 bits hit score in Blastp) to the known EST sequences in the database. Among the high identity-matched ESTs, 12S ribosomal RNA, actin 1, actin 2, arginine kinase and beta-actin were the most abundant transcripts with 5 to 20 times of hit. Primary hit sequences originate from shrimp, insects, lobsters, crabs and crayfish. The EST sequences were categorized as muscle structural proteins (25%), rRNA and protein synthesis (25%), followed by mitochondrial functions (22%), exoskeleton (14%), enzymes (6%) and RNA splicing (2%), suggesting abundant and diverse transcripts present in the shrimp abdominal muscle cDNA library.

Keywords

skeletal musclegene expressionESTgenomics
Type
Full Paper
Information
animal , Volume 2 , Issue 9 , September 2008 , pp. 1377 - 1383
Copyright
Copyright © The Animal Consortium 2008

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References

Alcivar-Warren, A 2001. ShrimpMap: a genetic approach to understand immune response and disease resistance in shrimp. In Proceedings of the Special Session on Sustainable Shrimp Culture, Aquaculture (ed. CL Browdy and DE Jory), pp. 174–189. The World Aquaculture Society, Baton Rouge, LA, USA.Google Scholar
Altschul, SF, Madden, TL, Schäffer, AA, Zhang, J, Zhang, Z, Miller, W, Lipman, DJ 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389–3402.Google Scholar
Bartlett, TC, Cuthbertson, BJ, Shepard, EF, Chapman, RW, Gross, PS, Warr, GW 2002. Crustins, homologues of an 11.5-kDa antibacterial peptide, from two species of penaeid shrimp, Litopenaeus vannamei and Litopenaeus setiferus. Marine Biotechnology 4, 278–293.Google Scholar
Bortoluzzi, S, Rampoldi, L, Simionati, B, Zimbello, R, Barbon, A, d’Alessi, F, Tiso, N, Pallavicini, A, Toppo, S, Cannata, N, Valle, G, Lanfranchi, G, Danieli, GA 1998. A comprehensive, high-resolution genomic transcript map of human skeletal muscle. Genome Research 8, 817–825.CrossRefGoogle ScholarPubMed
Cesar, JR, Yang, J 2007. Expression patterns of ubiquitin, heat shock protein 70, alpha-actin and beta-actin over the molt cycle in the abdominal muscle of marine shrimp Litopenaeus vannamei. Molecular Reproduction and Development 4, 554–559.Google Scholar
Cesar, JR, Zhao, B, Malecha, S, Ako, H, Yang, J 2006. Morphological and biochemical changes in the muscle of the marine shrimp Litopenaeus vannamei during the molt cycle. Aquaculture 261, 688–694.CrossRefGoogle Scholar
Davoli, R, Zambonelli, P, Bigi, D, Fontanesi, L, Russo, V 1999. Analysis of expressed sequence tags of porcine skeletal muscle. Gene 233, 181–188.Google Scholar
Dhar AK and Alcivar-Warren A 1997. Generation of expressed sequence tags (ESTs) from muscle cDNA library of shrimp (Penaeus vannamei). Proceedings of Plant & Animal Genome Mapping (PAG V), 12–16 January 1997, P324, p. 135. Conference, Town and Country Hotel San Diego, CA, USA.Google Scholar
Dhar AK, Fan Y, Murayama-Kayano E, Kayano T, Meisner R, Carr W, Breland V and Lotz J 2000. Isolation of expressed sequence tags (ESTs) from Taura Syndrome Virus (TSV)-challenged shrimp (Litopenaeus vannamei) by mRNA differential display. Proceedings of Plant and Animal Genome Mapping (PAG VIII) Conference, San Diego, CA, USA.Google Scholar
El Haj, AJ 1996. Crustacean genes involved in growth. In Gene regulation in aquatic organisms, SEB Seminar Series (ed. S Ennion and G Goldspink), pp. 94–112. Cambridge University Press, Cambridge, UK.Google Scholar
Gross, PS, Bartlett, TC, Browdy, CL, Chapman, RW, Warr, GW 2001. Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific white shrimp, Litopenaeus vannamei, and the Atlantic white shrimp, L. setiferus. Developmental and Comparative Immunology 25, 565–577.Google Scholar
Grosse, WM, Kappes, SM, McGraw, RA 2000. Linkage mapping and comparative analysis of bovine expressed sequence tags (ESTs). Animal Genetics 31, 171–177.Google Scholar
Koenders, A, Yu, X, Chang, ES, Mykles, DL 2002. Ubiquitin and actin expression in claw muscles of land crab, Geocarcinus lateralis, and american lobster, Homarus americanus: differential expression of ubiquitin in two slow muscle fiber types during molt-induced atrophy. Journal of Experimental Zoology 292, 618–632.Google Scholar
McKinsey, TA, Zhang, CL, Olson, EN 2002. Signaling chromatin to make muscle. Current Opinion in Cell Biology 14, 763–772.Google Scholar
Moore SS, Li C, Fu A, Meng Y, Murdoch G, Christopherson R and Dixon W 2001. Sequencing and characterization of adipose, skeletal muscle, hypothalamus, abomasums and duodenum cDNA libraries in Bos Taurus cattle. Plant & Animal Genome IX Conference, San Diego, CA, USA, 62pp.Google Scholar
Mykles, DL, Skinner, DM 1990. Atrophy of crustacean somatic muscle and the proteinases that do the job: a review. Journal of Crustacean Biology 10, 577–594.Google Scholar
Olson, EN, Klein, WH 1998. Muscle minus myoD. Developmental Biology 202, 153–156.Google Scholar
Tassanakajon, A, Klinbunga, S, Paunglarp, N, Rimphanitchayakit, V, Udomkit, A, Jitrapakdee, S, Sritunyalucksana, K, Phongdara, A, Pongsomboon, S, Supungul, P, Tang, S, Kuphanumart, K, Pichyangkura, R, Lursinsap, C 2006. Penaeus monodon gene discovery project: the generation of an EST, collection and establishment of a database. Gene 384, 104–112.Google Scholar
Wilson, K, Li, Y, Whan, V, Lehnert, S, Byrne, K, Moore, S, Pongsomboon, S, Tassanakajon, A, Rosenberg, G, Ballment, E, Fayazi, Z, Swan, J, Kenway, M, Benzie, J 2002. Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphisms. Aquaculture 204, 297–309.Google Scholar
Yamano, K, Tatsuya, U 2006. Expressed sequence tags from eyestalk of kuruma prawn Mrsupenaeus japonicus. Comparative Biochemistry and Physiology (A) 143, 155–161.Google Scholar
Yang, J, Ratovitski, T, Brady, JP, Solomon, MB, Wells, KD, Wall, RJ 2001. Expression of myostatin pro domain results in muscular transgenic mice. Molecular Reproduction and Development 60, 351–361.CrossRefGoogle ScholarPubMed
Yao, J, Coussens, PM, Saama, P, Suchyta, S, Ernst, CW 2002. Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Animal Biotechnology 13, 211–222.Google Scholar