CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Genomics Proteomics Bioinformatics. 2011 Apr;9(1-2):30-6. doi: 10.1016/S1672-0229(11)60005-3.
To enrich the genomic information of the commercially important fish species, we obtained 5,063 high-quality expressed sequence tags (ESTs) from the muscle cDNA database of the mandarin fish (Siniperca chuatsi). Clustering analysis yielded 1,625 unique sequences including 443 contigs (from 3,881 EST sequences) and 1,182 singletons. BLASTX searches showed that 959 unique sequences shared homology to proteins in the NCBI non-redundant database. A total of 740 unique sequences were functionally annotated using Gene Ontology. The 1,625 unique sequences were assigned to Kyoto Encyclopedia of Genes and Genomes reference pathways, and the results indicated that transcripts participating in nucleotide metabolism and amino acid metabolism are relatively abundant in S. chuatsi. Meanwhile, we identified 15 genes to be abundantly expressed in muscle of the mandarin fish. These genes are involved in muscle structural formation and regulation of muscle differentiation and development. The most remarkable gene in S. chuatsi is nuclease diphosphate kinase B, which is represented by 449 EST sequences accounting for 8.86% of the total EST sequences. Our work provides a transcript profile expressed in the white muscle of the mandarin fish, laying down a foundation in better understanding of fish genomics.
为了丰富商业上重要鱼类物种的基因组信息，我们从鳜鱼（Siniperca chuatsi）肌肉 cDNA 数据库中获得了 5063 条高质量的表达序列标签（EST）。聚类分析产生了 1625 条独特序列，包括 443 条重叠群（来自 3881 条 EST 序列）和 1182 条单序列。BLASTX 搜索表明，959 条独特序列与 NCBI 非冗余数据库中的蛋白质具有同源性。总共使用基因本体论对 740 个独特序列进行了功能注释。1625 个独特序列被分配到京都基因与基因组百科全书参考途径，结果表明参与核苷酸代谢和氨基酸代谢的转录物在 S. chuatsi 中相对丰富。同时，我们鉴定了 15 个在鳜鱼肌肉中大量表达的基因。这些基因参与肌肉结构的形成和肌肉分化与发育的调控。在 S. chuatsi 中最显著的基因是核酸二磷酸激酶 B，它由 449 条 EST 序列代表，占总 EST 序列的 8.86%。我们的工作提供了鳜鱼白肌中表达的转录谱，为更好地理解鱼类基因组学奠定了基础。
