title: Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database.
abstract: A large-scale expressed sequence tag (EST) sequencing project was undertaken for the purpose of gene discovery in the black tiger shrimp Penaeus monodon. Initially, 15 cDNA libraries were constructed from different tissues (eyestalk, hepatopancrease, haematopoietic tissue, haemocyte, lymphoid organ, and ovary) of shrimp, reared under normal or stress conditions, to identify tissue-specific genes and genes responding to infection and heat stress. A total of 10,100 clones were analyzed by single-pass sequencing from the 5' end. Clustering and assembling of these ESTs resulted in a total of 4845 unique sequences with 917 overlapping contigs and 3928 singletons. The redundancy of each cDNA library ranged from 13.4% to 61.3% with an overall redundancy of 61.1%. About half of these ESTs (2365 clones, 48.8%) showed significant homology (BLASTX, e-values <10(-4)) to known genes. A high proportion of P. monodon ESTs was most similar to the predicted protein sequences from various organisms, e.g. Homo sapiens (9%), Mus musculus (7%), Drosophila (6%), Gallus sp.(6%), and Anopheles (5%). Only 6% showed the highest similarity to other known genes from shrimp due to the limited sequence entries of the species in the public database. Several tissue-specific transcripts were identified as well as the candidate genes that may be implicated in the immune response. In addition, bioinformatic mining of microsatellites from the P. monodon ESTs identified 997 unique microsatellite containing ESTs in which 74 loci resided within the genes of known functions. Consequently, the P. monodon EST database was established. The EST sequence data and the BLAST results were stored and made available through a web-accessible database (). This EST database provides a useful resource for gene identification and functional genomic studies of shrimp.
authors.affiliation: Shrimp Molecular Biology and Genomics Laboratory, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. anchalee.k@chula.ac.th
authors.forename: Anchalee
authors.initials: A
authors.lastname: Tassanakajon
authors.forename: Sirawut
authors.initials: S
authors.lastname: Klinbunga
authors.forename: Narongsak
authors.initials: N
authors.lastname: Paunglarp
authors.forename: Vichien
authors.initials: V
authors.lastname: Rimphanitchayakit
authors.forename: Apinun
authors.initials: A
authors.lastname: Udomkit
authors.forename: Sarawut
authors.initials: S
authors.lastname: Jitrapakdee
authors.forename: Kallaya
authors.initials: K
authors.lastname: Sritunyalucksana
authors.forename: Amornrat
authors.initials: A
authors.lastname: Phongdara
authors.forename: Siriporn
authors.initials: S
authors.lastname: Pongsomboon
authors.forename: Premruethai
authors.initials: P
authors.lastname: Supungul
authors.forename: Sureerat
authors.initials: S
authors.lastname: Tang
authors.forename: Kasemsant
authors.initials: K
authors.lastname: Kuphanumart
authors.forename: Rath
authors.initials: R
authors.lastname: Pichyangkura
authors.forename: Chidchanok
authors.initials: C
authors.lastname: Lursinsap
mesh_terms: D000818:Animals; D018076:DNA, Complementary; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D016678:Genome; D023281:Genomics; D006434:Hemocytes / Q000378:metabolism; D008969:Molecular Sequence Data; D033561:Penaeidae / Q000235:genetics*
chemical_list: D018076:DNA, Complementary