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

Abstract

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.

Shrimp oncoprotein nm23 is a functional nucleoside diphosphate kinase

“…This result was confirmed in another transcriptome study from WSSV-challenged organisms (Leu et al 2011).…”

“…The deduced amino acid sequence shares 72% and 77% identity with B. mori and H. sapiens, respectively. sNDK is overexpressed during WSSV infection (Clavero-Salas et al 2007;Leu et al 2011), but its biochemical activity has not been demonstrated yet.…”

RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei

“…Such progress included the development of molecular markers (Leu et al, 2011;Duan et al, 2013), generation of large-insert BAC libraries , construction of genetic and physical maps, and efforts for sequencing the entire genome of the penaeid shrimp (Shen et al, 2007;Du et al, 2010;You et al, 2010;Lin et al, 2012). These genomic resources made it possible to address the issues of disease resistance at the genome and transcriptome levels using various approaches such as microarrays (Zeng and Lu, 2009;Aoki et al, 2011).…”

Multiple isoforms of immune-related genes from hemocytes and eyestalk cDNA libraries of swimming crab Portunus trituberculatus

“…EST databases are rich resources for gene expression analysis, and can provide an informative overview of major transcripts in specific tissues. Many tissue-specific genes and expression profiles have been successfully characterized, which are highly useful in understanding the gene functions, tissue physiology and transcriptomics [2,9,10].…”

“…The cDNA library construction and expressed sequence tags (ESTs) analysis are efficient approaches to collect genomic information and identify useful genes [1,2]. They were developed originally to discover new human genes [1], but now are extensively used for studying genomics of important aquaculture animals including fishes [3,4], shrimps [5,6] and crabs [7,8].…”