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A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data.

Duan X, Yi S, Guo X, Wang W - Int J Mol Sci (2015)

Bottom Line: Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG), as well as low-frequency ones (NUA and NCG codons) were identified.Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis.This work provided new insights into fish biology and new information for breeding projects.

View Article: PubMed Central - PubMed

Affiliation: College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China. xiaokeduan@126.com.

ABSTRACT
Blunt snout bream (Megalobrama amblycephala) is an important fish species for its delicacy and high economic value in China. Codon usage analysis could be helpful to understand its codon biology, mRNA translation and vertebrate evolution. Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG), as well as low-frequency ones (NUA and NCG codons) were identified. A total of 724 high-frequency codon pairs were observed. Meanwhile, 14 preferred and 199 avoided neighboring codon pairs were also identified, but bias was almost not shown with one or more intervening codons inserted between the same pairs. Codon usage bias in the regions close to start and stop codons indicated apparent heterogeneity, which even occurs in the flanking nucleotide sequence. Codon usage bias (RSCU and SCUO) was related to GC3 (GC content of 3rd nucleotide in codon) bias. Six GO (Gene ontology) categories and the number of methylation targets were influenced by GC3. Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis. This work provided new insights into fish biology and new information for breeding projects.

No MeSH data available.


Related in: MedlinePlus

Correlation between GC3 content and codon usage bias (RSCU and SCUO) in M. amblycephala. (A) The PCA analysis of RSCU of 59 codons from 646 ORFs on the primary and secondary axes (accounting for 16.61% and 4.79% of the total variations, respectively) and demonstration by 6 GC3 levels; (B) SCUO versus GC3 plot with polynomial fitting.
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ijms-16-11996-f005: Correlation between GC3 content and codon usage bias (RSCU and SCUO) in M. amblycephala. (A) The PCA analysis of RSCU of 59 codons from 646 ORFs on the primary and secondary axes (accounting for 16.61% and 4.79% of the total variations, respectively) and demonstration by 6 GC3 levels; (B) SCUO versus GC3 plot with polynomial fitting.

Mentions: GC3 content varied across M. amblycephala transcripts, and its distribution showed a predominantly unimodal type (Figure S2A), which was similar to the earlier observation on other cold-blooded animals [31]. All M. amblycephala 646 ORF sequences were performed using PCA based on RSCU to measure the codon usage bias among genes (Figure 5A). Transcripts with different GC3 contents could be separated mainly along the first axis, although the percentage of contribution of the axes is somewhat low. These similar correlations have also been reported in some plants [7,32]. SCUO, another index to measure codon usage bias among genes, showed a strong ā€œUā€ nonlinear correlation with GC3 (Figure 5B), similar to the situation in unicellular, human and mouse genomes [33,34]. Above all, codon usage bias showed the pronounced differences across M. amblycephala transcripts and had some correlation with GC3 content.


A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data.

Duan X, Yi S, Guo X, Wang W - Int J Mol Sci (2015)

Correlation between GC3 content and codon usage bias (RSCU and SCUO) in M. amblycephala. (A) The PCA analysis of RSCU of 59 codons from 646 ORFs on the primary and secondary axes (accounting for 16.61% and 4.79% of the total variations, respectively) and demonstration by 6 GC3 levels; (B) SCUO versus GC3 plot with polynomial fitting.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4490425&req=5

ijms-16-11996-f005: Correlation between GC3 content and codon usage bias (RSCU and SCUO) in M. amblycephala. (A) The PCA analysis of RSCU of 59 codons from 646 ORFs on the primary and secondary axes (accounting for 16.61% and 4.79% of the total variations, respectively) and demonstration by 6 GC3 levels; (B) SCUO versus GC3 plot with polynomial fitting.
Mentions: GC3 content varied across M. amblycephala transcripts, and its distribution showed a predominantly unimodal type (Figure S2A), which was similar to the earlier observation on other cold-blooded animals [31]. All M. amblycephala 646 ORF sequences were performed using PCA based on RSCU to measure the codon usage bias among genes (Figure 5A). Transcripts with different GC3 contents could be separated mainly along the first axis, although the percentage of contribution of the axes is somewhat low. These similar correlations have also been reported in some plants [7,32]. SCUO, another index to measure codon usage bias among genes, showed a strong ā€œUā€ nonlinear correlation with GC3 (Figure 5B), similar to the situation in unicellular, human and mouse genomes [33,34]. Above all, codon usage bias showed the pronounced differences across M. amblycephala transcripts and had some correlation with GC3 content.

Bottom Line: Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG), as well as low-frequency ones (NUA and NCG codons) were identified.Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis.This work provided new insights into fish biology and new information for breeding projects.

View Article: PubMed Central - PubMed

Affiliation: College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China. xiaokeduan@126.com.

ABSTRACT
Blunt snout bream (Megalobrama amblycephala) is an important fish species for its delicacy and high economic value in China. Codon usage analysis could be helpful to understand its codon biology, mRNA translation and vertebrate evolution. Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG), as well as low-frequency ones (NUA and NCG codons) were identified. A total of 724 high-frequency codon pairs were observed. Meanwhile, 14 preferred and 199 avoided neighboring codon pairs were also identified, but bias was almost not shown with one or more intervening codons inserted between the same pairs. Codon usage bias in the regions close to start and stop codons indicated apparent heterogeneity, which even occurs in the flanking nucleotide sequence. Codon usage bias (RSCU and SCUO) was related to GC3 (GC content of 3rd nucleotide in codon) bias. Six GO (Gene ontology) categories and the number of methylation targets were influenced by GC3. Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis. This work provided new insights into fish biology and new information for breeding projects.

No MeSH data available.


Related in: MedlinePlus