Dataset Information

EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).

ABSTRACT: 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.

SUBMITTER: Ding F

PROVIDER: S-EPMC5054145 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).

Ding Feng F Chu Wuying W Cui Peng P Tao Meng M Zhou Ruixue R Zhao Falan F Hu Songnian S Zhang Jianshe J

Genomics, proteomics & bioinformatics 20110401 1-2

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 ann ...[more]

PMID: 21641560

Similar Datasets

Project description:Social learning plays important roles in gaining new foraging skills and food preferences. However, the potential role and molecular mechanism of social learning in acquiring new feeding habits is less clear in fish. In the present study, we examined the success rate of feeding habit domestication from live prey fish to dead prey fish, as well as the food intake of dead prey fish in mandarin fish with or without feeders of dead prey fish as demonstrators. Here, we found that mandarin fish can learn from each other how to solve novel foraging tasks, feeding on dead prey fish. In addition, the analysis of gene expressions and signaling pathways of learning through Western blotting and transcriptome sequencing shows that the expression of the c-fos, fra2, zif268, c/ebpd and sytIV genes were significantly increased, and the anorexigenic pomc and leptin a expressions were decreased in fish of the learning group. The phosphorylation levels of protein kinase A (PKA) and Ca2+/calmodulin-dependent protein kinase II (CaMKII) in the learning group were significantly higher than those of the control group, while the phosphorylation level of S6 ribosomal protein (S6) was lower. With the inhibitors of PKA and CaMKII signaling and the chromatin immunoprecipitation (ChIP) assay, we further found that the social learning of new feeding habits in mandarin fish could be attributed to the activation of the CaMKII signaling pathway and then the stimulation of the expression of the c-fos gene, which might be an important transcriptional factor to inhibit the expression of the anorexigenic gene pomc, resulting in the food intake of dead prey fish in mandarin fish. Altogether, our results support the hypothesis that social learning could facilitate the acquisition of novel feeding habits in fish, and it considerably increases the rate of subsequent individual food intake and domestication through the interaction between the learning gene c-fos and the appetite control gene pomc.

Dataset Information

EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).

Publications

EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets