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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

Overview of preferred and avoided codon pairs in M. amblycephala. (A–F) The relationship between observed frequency and expected frequency of 3721 (61 × 61) codon pairs (excluding stop codons). The red, green and black spots represent the preferred codon pairs, avoided codon pairs and unbiased codon pairs, respectively. The lowest p-value was set to 1 × 10−10. (A) The ratio of observed frequency to expected frequency for neighboring codon pairs; The ratio of observed frequency to expected frequency for codon pairs separated by one (B); two (C); three (D); four (E) and five (F) intervening codons; (G) Distribution of the ratio of observed frequency to expected frequency for different neighboring codon pairs. The X axis shows the dinucleotide at the junction of neighboring codon pairs.
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ijms-16-11996-f002: Overview of preferred and avoided codon pairs in M. amblycephala. (A–F) The relationship between observed frequency and expected frequency of 3721 (61 × 61) codon pairs (excluding stop codons). The red, green and black spots represent the preferred codon pairs, avoided codon pairs and unbiased codon pairs, respectively. The lowest p-value was set to 1 × 10−10. (A) The ratio of observed frequency to expected frequency for neighboring codon pairs; The ratio of observed frequency to expected frequency for codon pairs separated by one (B); two (C); three (D); four (E) and five (F) intervening codons; (G) Distribution of the ratio of observed frequency to expected frequency for different neighboring codon pairs. The X axis shows the dinucleotide at the junction of neighboring codon pairs.

Mentions: Based on the observed and expected frequency of all 3721 neighboring codon pairs (61 × 61) without the constraint of synonymous codon pairs, 14 preferred codon pairs and 199 avoided codon pairs were observed by using SC (shuffled codons) model (Figure 2A). The number of avoided codon pairs was much larger than preferred codon pairs suggesting that the selection acts primarily through avoidance of the most disadvantageous codon pairs [18]. However the bias nearly disappeared when one to five intervening codons inserted between the pairs were tested (Figure 2B–F, Supplementary file 2). This phenomenon is consistent with the mechanism that neighboring codon pair bias may have significance in protein synthesis [19].


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)

Overview of preferred and avoided codon pairs in M. amblycephala. (A–F) The relationship between observed frequency and expected frequency of 3721 (61 × 61) codon pairs (excluding stop codons). The red, green and black spots represent the preferred codon pairs, avoided codon pairs and unbiased codon pairs, respectively. The lowest p-value was set to 1 × 10−10. (A) The ratio of observed frequency to expected frequency for neighboring codon pairs; The ratio of observed frequency to expected frequency for codon pairs separated by one (B); two (C); three (D); four (E) and five (F) intervening codons; (G) Distribution of the ratio of observed frequency to expected frequency for different neighboring codon pairs. The X axis shows the dinucleotide at the junction of neighboring codon pairs.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f002: Overview of preferred and avoided codon pairs in M. amblycephala. (A–F) The relationship between observed frequency and expected frequency of 3721 (61 × 61) codon pairs (excluding stop codons). The red, green and black spots represent the preferred codon pairs, avoided codon pairs and unbiased codon pairs, respectively. The lowest p-value was set to 1 × 10−10. (A) The ratio of observed frequency to expected frequency for neighboring codon pairs; The ratio of observed frequency to expected frequency for codon pairs separated by one (B); two (C); three (D); four (E) and five (F) intervening codons; (G) Distribution of the ratio of observed frequency to expected frequency for different neighboring codon pairs. The X axis shows the dinucleotide at the junction of neighboring codon pairs.
Mentions: Based on the observed and expected frequency of all 3721 neighboring codon pairs (61 × 61) without the constraint of synonymous codon pairs, 14 preferred codon pairs and 199 avoided codon pairs were observed by using SC (shuffled codons) model (Figure 2A). The number of avoided codon pairs was much larger than preferred codon pairs suggesting that the selection acts primarily through avoidance of the most disadvantageous codon pairs [18]. However the bias nearly disappeared when one to five intervening codons inserted between the pairs were tested (Figure 2B–F, Supplementary file 2). This phenomenon is consistent with the mechanism that neighboring codon pair bias may have significance in protein synthesis [19].

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