Tassanakajon Anchalee, Klinbunga Sirawut, Paunglarp Narongsak, Rimphanitchayakit Vichien, Udomkit Apinun, Jitrapakdee Sarawut, Sritunyalucksana Kallaya, Phongdara Amornrat, Pongsomboon Siriporn, Supungul Premruethai, Tang Sureerat, Kuphanumart Kasemsant, Pichyangkura Rath, Lursinsap Chidchanok
Shrimp Molecular Biology and Genomics Laboratory, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Gene. 2006 Dec 15;384:104-12. doi: 10.1016/j.gene.2006.07.012. Epub 2006 Jul 28.
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.
为了在黑虎虾（斑节对虾）中发现基因，开展了一项大规模表达序列标签（EST）测序项目。最初，从正常或应激条件下饲养的虾的不同组织（眼柄、肝胰腺、造血组织、血细胞、淋巴器官和卵巢）构建了15个cDNA文库，以鉴定组织特异性基因以及对感染和热应激作出反应的基因。从5'端对总共10100个克隆进行了单通道测序分析。这些EST的聚类和组装产生了总共4845个独特序列，其中包括917个重叠群和3928个单拷贝序列。每个cDNA文库的冗余度在13.4%至61.3%之间，总体冗余度为61.1%。这些EST中约一半（2365个克隆，48.8%）与已知基因具有显著同源性（BLASTX，e值<10^(-4)）。斑节对虾EST的很大一部分与来自各种生物的预测蛋白质序列最相似，例如人类（9%）、小家鼠（7%）、果蝇（6%）、鸡（6%）和按蚊（5%）。由于该物种在公共数据库中的序列条目有限，只有6%与来自虾的其他已知基因具有最高相似性。鉴定出了几个组织特异性转录本以及可能与免疫反应有关的候选基因。此外，从斑节对虾EST中对微卫星进行生物信息学挖掘，鉴定出997个含有独特微卫星的EST，其中74个位点位于已知功能的基因内。因此，建立了斑节对虾EST数据库。EST序列数据和BLAST结果通过一个可通过网络访问的数据库进行存储并可供使用。这个EST数据库为虾的基因鉴定和功能基因组学研究提供了有用的资源。
