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Transcriptome Analysis of Blunt Snout Bream (Megalobrama amblycephala) Reveals Putative Differential Expression Genes Related to Growth and Hypoxia.

Li FG, Chen J, Jiang XY, Zou SM - PLoS ONE (2015)

Bottom Line: A total of 31,338 transcripts from the same locus (unigenes) were annotated and assigned to 104 functional groups, and 23,103 unigenes were classified into seven main categories, including 45 secondary KEGG pathways.A total of 22,255 (71%) known putative unigenes were found to be shared across the genomes of five model fish species and mammals, and a substantial number (9.4%) of potentially novel genes were identified.When 6,639 unigenes were used in the analysis of differential expression (DE) genes, the number of putative DE genes related to growth pathways in FH, SH, SN and FN was 159, 118, 92 and 65 in both the liver and gills, respectively, and the number of DE genes related to hypoxic response was 57, 33, 23 and 21 in FH, FN, SH and SN, respectively.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.

ABSTRACT
The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture species, but it is sensitive to hypoxia. No transcriptome data related to growth and hypoxia response are available for this species. In this study, we performed de novo transcriptome sequencing for the liver and gills of the fast-growth family and slow-growth family derived from 'Pujiang No.1' F10 blunt snout bream that were under hypoxic stress and normoxia, respectively. The fish were divided into the following 4 groups: fast-growth family under hypoxic stress, FH; slow-growth family under hypoxic stress, SH; fast-growth family under normoxia, FN; and slow-growth family under normoxia, SN. A total of 185 million high-quality reads were obtained from the normalized cDNA of the pooled samples, which were assembled into 465,582 contigs and 237,172 transcripts. A total of 31,338 transcripts from the same locus (unigenes) were annotated and assigned to 104 functional groups, and 23,103 unigenes were classified into seven main categories, including 45 secondary KEGG pathways. A total of 22,255 (71%) known putative unigenes were found to be shared across the genomes of five model fish species and mammals, and a substantial number (9.4%) of potentially novel genes were identified. When 6,639 unigenes were used in the analysis of differential expression (DE) genes, the number of putative DE genes related to growth pathways in FH, SH, SN and FN was 159, 118, 92 and 65 in both the liver and gills, respectively, and the number of DE genes related to hypoxic response was 57, 33, 23 and 21 in FH, FN, SH and SN, respectively. Our results suggest that growth performance of the fast-growth family should be due to complex mutual gene regulatory mechanisms of these putative DE genes between growth and hypoxia.

No MeSH data available.


Related in: MedlinePlus

Classification of unigenes on the basis of KEGG categorization.
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pone.0142801.g004: Classification of unigenes on the basis of KEGG categorization.

Mentions: Functional classification of KEGG provided a valuable resource for investigating specific processes and pathways in the liver and gills of the blunt snout bream. A total of 23,103 unigenes were classified into seven main categories, including 45 secondary pathways in the eight tested samples (Fig 4). Human diseases was the largest category (7,006, 30.33%), followed by organismal systems (5,907, 25.57%), metabolism (3,372, 14.6%), environmental information processing (2,567, 11.11%), and cellular processes (2,502, 10.82%); genetic information processing (1,749, 7.57%) was the smallest category (Fig 4). These results indicate that active metabolic and genetic processes affected by dissolved oxygen levels occur in the liver and gills of the blunt snout bream.


Transcriptome Analysis of Blunt Snout Bream (Megalobrama amblycephala) Reveals Putative Differential Expression Genes Related to Growth and Hypoxia.

Li FG, Chen J, Jiang XY, Zou SM - PLoS ONE (2015)

Classification of unigenes on the basis of KEGG categorization.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4640810&req=5

pone.0142801.g004: Classification of unigenes on the basis of KEGG categorization.
Mentions: Functional classification of KEGG provided a valuable resource for investigating specific processes and pathways in the liver and gills of the blunt snout bream. A total of 23,103 unigenes were classified into seven main categories, including 45 secondary pathways in the eight tested samples (Fig 4). Human diseases was the largest category (7,006, 30.33%), followed by organismal systems (5,907, 25.57%), metabolism (3,372, 14.6%), environmental information processing (2,567, 11.11%), and cellular processes (2,502, 10.82%); genetic information processing (1,749, 7.57%) was the smallest category (Fig 4). These results indicate that active metabolic and genetic processes affected by dissolved oxygen levels occur in the liver and gills of the blunt snout bream.

Bottom Line: A total of 31,338 transcripts from the same locus (unigenes) were annotated and assigned to 104 functional groups, and 23,103 unigenes were classified into seven main categories, including 45 secondary KEGG pathways.A total of 22,255 (71%) known putative unigenes were found to be shared across the genomes of five model fish species and mammals, and a substantial number (9.4%) of potentially novel genes were identified.When 6,639 unigenes were used in the analysis of differential expression (DE) genes, the number of putative DE genes related to growth pathways in FH, SH, SN and FN was 159, 118, 92 and 65 in both the liver and gills, respectively, and the number of DE genes related to hypoxic response was 57, 33, 23 and 21 in FH, FN, SH and SN, respectively.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.

ABSTRACT
The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture species, but it is sensitive to hypoxia. No transcriptome data related to growth and hypoxia response are available for this species. In this study, we performed de novo transcriptome sequencing for the liver and gills of the fast-growth family and slow-growth family derived from 'Pujiang No.1' F10 blunt snout bream that were under hypoxic stress and normoxia, respectively. The fish were divided into the following 4 groups: fast-growth family under hypoxic stress, FH; slow-growth family under hypoxic stress, SH; fast-growth family under normoxia, FN; and slow-growth family under normoxia, SN. A total of 185 million high-quality reads were obtained from the normalized cDNA of the pooled samples, which were assembled into 465,582 contigs and 237,172 transcripts. A total of 31,338 transcripts from the same locus (unigenes) were annotated and assigned to 104 functional groups, and 23,103 unigenes were classified into seven main categories, including 45 secondary KEGG pathways. A total of 22,255 (71%) known putative unigenes were found to be shared across the genomes of five model fish species and mammals, and a substantial number (9.4%) of potentially novel genes were identified. When 6,639 unigenes were used in the analysis of differential expression (DE) genes, the number of putative DE genes related to growth pathways in FH, SH, SN and FN was 159, 118, 92 and 65 in both the liver and gills, respectively, and the number of DE genes related to hypoxic response was 57, 33, 23 and 21 in FH, FN, SH and SN, respectively. Our results suggest that growth performance of the fast-growth family should be due to complex mutual gene regulatory mechanisms of these putative DE genes between growth and hypoxia.

No MeSH data available.


Related in: MedlinePlus