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

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.