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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.

Show MeSH
Conservation of M. amblycephala gene identities with other species.Number of M. amblycephala homologous genes identified from other species using BLASTX searches.
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pone-0042637-g005: Conservation of M. amblycephala gene identities with other species.Number of M. amblycephala homologous genes identified from other species using BLASTX searches.

Mentions: To assess the evolutionary conservation of the identified unique genes, the number of hits to unique genes in each species of zebrafish, medaka, Tetraodon, Fugu, stickleback, human, mouse, and chicken were compared. A total of 27,488 (65.4% of total number of unique M. amblycephala genes) putative known unique genes were found in all eight species; 30,332 (72.2%) were found in all five fish species; and 41,229 (98.1%) were found in at least one of the five fish species (Figure 5), indicating a high level of conservation of gene content among M. amblycephala and other teleost fish species.


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)

Conservation of M. amblycephala gene identities with other species.Number of M. amblycephala homologous genes identified from other species using BLASTX searches.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042637-g005: Conservation of M. amblycephala gene identities with other species.Number of M. amblycephala homologous genes identified from other species using BLASTX searches.
Mentions: To assess the evolutionary conservation of the identified unique genes, the number of hits to unique genes in each species of zebrafish, medaka, Tetraodon, Fugu, stickleback, human, mouse, and chicken were compared. A total of 27,488 (65.4% of total number of unique M. amblycephala genes) putative known unique genes were found in all eight species; 30,332 (72.2%) were found in all five fish species; and 41,229 (98.1%) were found in at least one of the five fish species (Figure 5), indicating a high level of conservation of gene content among M. amblycephala and other teleost fish species.

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