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Transcriptome analysis and SSR/SNP markers information of the blunt snout bream (Megalobrama amblycephala).

Gao Z, Luo W, Liu H, Zeng C, Liu X, Yi S, Wang W - PLoS ONE (2012)

Bottom Line: A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized.A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Freshwater Animal Breeding, College of Fisheries, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.

ABSTRACT

Background: Blunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. Right now, only limited EST resources were available for M. amblycephala. Recent advances in large-scale RNA sequencing provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes.

Methodology and principal findings: Using 454 pyrosequencing, a total of 1,409,706 high quality reads (total length 577 Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals. These sequences were assembled into 26,802 contigs and 73,675 singletons. After BLAST searches against the NCBI non-redundant (NR) and UniProt databases with an arbitrary expectation value of E(-10), over 40,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, tetraodon, fugu, stickleback, human, mouse, and chicken, and identified a substantial number of potentially novel M. amblycephala genes. A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized. A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.

Conclusions: This study is the first comprehensive transcriptome analysis for a fish species belonging to the genus Megalobrama. These large EST resources are expected to be valuable for the development of molecular markers, construction of gene-based linkage map, and large-scale expression analysis of M. amblycephala, as well as comparative genome analysis for the genus Megalobrama fish species. The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

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Gene ontology assignments for M. amblycephala.The annotated contigs and singletons from M. amblycephala 454 sequencing that matched various gene ontology (GO) categories.
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pone-0042637-g004: Gene ontology assignments for M. amblycephala.The annotated contigs and singletons from M. amblycephala 454 sequencing that matched various gene ontology (GO) categories.

Mentions: BLAST searches for all contigs and singletons obtained from M. amblycephala were performed against the nr protein database using the BLASTx algorithm and an arbitrary expectation value of E−10 (Table S1). Among a total 100,477 unigenes (contigs and singletons), 40,687 (40.5%) showed at least one significant alignment to an existing gene model. The assembled transcripts were annotated against UniProt (Table S2). Of the 26,802 contigs, 17,378 (64.8%) returned an above cut-off Blast hits to the Uniprot database and the average length of these contigs was 803 bp. As for the 19,866 contigs with the length more than 500 bp, 13,915 (70.0%) showed significant hits to the Uniprot database. Of the 73,675 singletons, 24,629 sequences (33.4%) had Blast hits to the Uniprot database and the average read length of these singletons was 424 bp. Altogether, of the 100,477 unigenes, 42,007 (41.8%) had significant BLASTx hits to the Uniprot database and matched 20,674 unique protein accessions (Table 2). Gene ontology terms of biological processes, molecular functions and cellular components were showed in Figure 4. A large number of unigenes were assigned to a wide range of gene ontology categories.


Transcriptome analysis and SSR/SNP markers information of the blunt snout bream (Megalobrama amblycephala).

Gao Z, Luo W, Liu H, Zeng C, Liu X, Yi S, Wang W - PLoS ONE (2012)

Gene ontology assignments for M. amblycephala.The annotated contigs and singletons from M. amblycephala 454 sequencing that matched various gene ontology (GO) categories.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412804&req=5

pone-0042637-g004: Gene ontology assignments for M. amblycephala.The annotated contigs and singletons from M. amblycephala 454 sequencing that matched various gene ontology (GO) categories.
Mentions: BLAST searches for all contigs and singletons obtained from M. amblycephala were performed against the nr protein database using the BLASTx algorithm and an arbitrary expectation value of E−10 (Table S1). Among a total 100,477 unigenes (contigs and singletons), 40,687 (40.5%) showed at least one significant alignment to an existing gene model. The assembled transcripts were annotated against UniProt (Table S2). Of the 26,802 contigs, 17,378 (64.8%) returned an above cut-off Blast hits to the Uniprot database and the average length of these contigs was 803 bp. As for the 19,866 contigs with the length more than 500 bp, 13,915 (70.0%) showed significant hits to the Uniprot database. Of the 73,675 singletons, 24,629 sequences (33.4%) had Blast hits to the Uniprot database and the average read length of these singletons was 424 bp. Altogether, of the 100,477 unigenes, 42,007 (41.8%) had significant BLASTx hits to the Uniprot database and matched 20,674 unique protein accessions (Table 2). Gene ontology terms of biological processes, molecular functions and cellular components were showed in Figure 4. A large number of unigenes were assigned to a wide range of gene ontology categories.

Bottom Line: A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized.A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Freshwater Animal Breeding, College of Fisheries, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.

ABSTRACT

Background: Blunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. Right now, only limited EST resources were available for M. amblycephala. Recent advances in large-scale RNA sequencing provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes.

Methodology and principal findings: Using 454 pyrosequencing, a total of 1,409,706 high quality reads (total length 577 Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals. These sequences were assembled into 26,802 contigs and 73,675 singletons. After BLAST searches against the NCBI non-redundant (NR) and UniProt databases with an arbitrary expectation value of E(-10), over 40,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, tetraodon, fugu, stickleback, human, mouse, and chicken, and identified a substantial number of potentially novel M. amblycephala genes. A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized. A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.

Conclusions: This study is the first comprehensive transcriptome analysis for a fish species belonging to the genus Megalobrama. These large EST resources are expected to be valuable for the development of molecular markers, construction of gene-based linkage map, and large-scale expression analysis of M. amblycephala, as well as comparative genome analysis for the genus Megalobrama fish species. The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

Show MeSH