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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

Heat map and PCA analysis of RSCU of synonymous codons from 23 vertebrate species. (A) Heat map of adjusted RSCU of 59 codons from 23 species using Euclidean distance and average linkage clustering module; (B) The PCA analysis of RSCU of 59 codons from 23 species on the primary and secondary axes (accounting for 80.91% and 10.81% of the total variation, respectively). Dark cyan, blue, red, black represent the fishes, reptile together with amphibian, birds and mammals, respectively; (C) Variance contribution ratio (bar) and accumulated variance contribution ratio (triangular plot) of the first ten principal components (X-axis) of (B).
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ijms-16-11996-f007: Heat map and PCA analysis of RSCU of synonymous codons from 23 vertebrate species. (A) Heat map of adjusted RSCU of 59 codons from 23 species using Euclidean distance and average linkage clustering module; (B) The PCA analysis of RSCU of 59 codons from 23 species on the primary and secondary axes (accounting for 80.91% and 10.81% of the total variation, respectively). Dark cyan, blue, red, black represent the fishes, reptile together with amphibian, birds and mammals, respectively; (C) Variance contribution ratio (bar) and accumulated variance contribution ratio (triangular plot) of the first ten principal components (X-axis) of (B).

Mentions: A heat map via bi-clustering was used to describe the variations of codon usage bias among 23 vertebrate species based on the RSCU of all 59 synonymous codons (Figure 7A). Mammals and most fishes were clustered in a group, while birds, reptile, amphibian and two fishes (M. amblycephala and D. rerio) were clustered in another. However, the PCA (principal component analysis) test separated these four vertebrate taxonomic groups with the first two principal components (two axes), which account for 80.91% and 10.81% of variations, respectively. The fish group is more scattered than other groups, implying that this group contains much higher variations (Figure 7B,C).


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)

Heat map and PCA analysis of RSCU of synonymous codons from 23 vertebrate species. (A) Heat map of adjusted RSCU of 59 codons from 23 species using Euclidean distance and average linkage clustering module; (B) The PCA analysis of RSCU of 59 codons from 23 species on the primary and secondary axes (accounting for 80.91% and 10.81% of the total variation, respectively). Dark cyan, blue, red, black represent the fishes, reptile together with amphibian, birds and mammals, respectively; (C) Variance contribution ratio (bar) and accumulated variance contribution ratio (triangular plot) of the first ten principal components (X-axis) of (B).
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f007: Heat map and PCA analysis of RSCU of synonymous codons from 23 vertebrate species. (A) Heat map of adjusted RSCU of 59 codons from 23 species using Euclidean distance and average linkage clustering module; (B) The PCA analysis of RSCU of 59 codons from 23 species on the primary and secondary axes (accounting for 80.91% and 10.81% of the total variation, respectively). Dark cyan, blue, red, black represent the fishes, reptile together with amphibian, birds and mammals, respectively; (C) Variance contribution ratio (bar) and accumulated variance contribution ratio (triangular plot) of the first ten principal components (X-axis) of (B).
Mentions: A heat map via bi-clustering was used to describe the variations of codon usage bias among 23 vertebrate species based on the RSCU of all 59 synonymous codons (Figure 7A). Mammals and most fishes were clustered in a group, while birds, reptile, amphibian and two fishes (M. amblycephala and D. rerio) were clustered in another. However, the PCA (principal component analysis) test separated these four vertebrate taxonomic groups with the first two principal components (two axes), which account for 80.91% and 10.81% of variations, respectively. The fish group is more scattered than other groups, implying that this group contains much higher variations (Figure 7B,C).

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