Limits...
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.


Position-dependent codon usage bias in M. amblycephala. KLD value for each codon in M. amblycephala is depicted according to the scaled color bar on the right as a function of position: 5 bins following the start codon and 5 bins before stop codons. Rare codons and abundant codons are marked green and red, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4490425&req=5

ijms-16-11996-f003: Position-dependent codon usage bias in M. amblycephala. KLD value for each codon in M. amblycephala is depicted according to the scaled color bar on the right as a function of position: 5 bins following the start codon and 5 bins before stop codons. Rare codons and abundant codons are marked green and red, respectively.

Mentions: It is widely reported that codon usage bias is not uniform with regard to the position within genes [22,23]. In M. amblycephala, the visual analysis of KLD (Kullback–Leibler divergence) values for each codon at the 5ʹ end and 3ʹ end reveals position-dependent heterogeneity (Figure 3). The majority of rare codons were enriched at the beginning of genes and abundant codons were the reverse. Meanwhile, the first 10 codons following the AUG had a preferential selection with A or U at the third position (AU3) (Figure S1A). The phenomena could be explained by suppressing mRNA structure and reducing folding propensity for efficient translation initiation [23]. Altogether, the higher values of KLD than a model indicates an unusual codon usage N- or C-terminal regions (Figure 3, Figure S1B).


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)

Position-dependent codon usage bias in M. amblycephala. KLD value for each codon in M. amblycephala is depicted according to the scaled color bar on the right as a function of position: 5 bins following the start codon and 5 bins before stop codons. Rare codons and abundant codons are marked green and red, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f003: Position-dependent codon usage bias in M. amblycephala. KLD value for each codon in M. amblycephala is depicted according to the scaled color bar on the right as a function of position: 5 bins following the start codon and 5 bins before stop codons. Rare codons and abundant codons are marked green and red, respectively.
Mentions: It is widely reported that codon usage bias is not uniform with regard to the position within genes [22,23]. In M. amblycephala, the visual analysis of KLD (Kullback–Leibler divergence) values for each codon at the 5ʹ end and 3ʹ end reveals position-dependent heterogeneity (Figure 3). The majority of rare codons were enriched at the beginning of genes and abundant codons were the reverse. Meanwhile, the first 10 codons following the AUG had a preferential selection with A or U at the third position (AU3) (Figure S1A). The phenomena could be explained by suppressing mRNA structure and reducing folding propensity for efficient translation initiation [23]. Altogether, the higher values of KLD than a model indicates an unusual codon usage N- or C-terminal regions (Figure 3, Figure S1B).

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.