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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.


Unequal usage of 64 codons in M. amblycephala. The codons for the same amino acids are listed on the left and are colored yellow, orange yellow, orange and red to show occurrence frequencies of 0.0‰–10.0‰, 10.0‰–20.0‰, 20.0‰–30.0‰, and over 30.0‰, respectively. The data is shown as a triplet codon (RSCU, relative synonymous codon usage), and high-frequency codons are underlined.
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ijms-16-11996-f001: Unequal usage of 64 codons in M. amblycephala. The codons for the same amino acids are listed on the left and are colored yellow, orange yellow, orange and red to show occurrence frequencies of 0.0‰–10.0‰, 10.0‰–20.0‰, 20.0‰–30.0‰, and over 30.0‰, respectively. The data is shown as a triplet codon (RSCU, relative synonymous codon usage), and high-frequency codons are underlined.

Mentions: A codon usage table was created by investigating all 138,002 codons (Table S1 in Supplementary file 1). With each codon, excepting three stop codons, GAG was most frequently presented, with the occurrence of 45.8‰, 2.8 times the average frequency. UCG was the lowest frequency codon (4.4‰) and another 14 codons also had low frequency (<10‰) (Figure 1). Measured by their codon frequencies, abundant and rare codons were defined as the 15 most abundant and 15 most rare codons in M. amblycephala. The overall GC content in the study is 0.494, but it varies among different codon positions, with the highest in GC3 (GC content of 3rd nucleotide in codons), at a value of 0.558, lowest in GC2 (GC content of 2nd nucleotide in codons), at a value of 0.389, and intermediate in GC1 (GC content of 1st nucleotide in codons), at a value of 0.534, which is consistent with the observations in other fishes (Table S2).


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)

Unequal usage of 64 codons in M. amblycephala. The codons for the same amino acids are listed on the left and are colored yellow, orange yellow, orange and red to show occurrence frequencies of 0.0‰–10.0‰, 10.0‰–20.0‰, 20.0‰–30.0‰, and over 30.0‰, respectively. The data is shown as a triplet codon (RSCU, relative synonymous codon usage), and high-frequency codons are underlined.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f001: Unequal usage of 64 codons in M. amblycephala. The codons for the same amino acids are listed on the left and are colored yellow, orange yellow, orange and red to show occurrence frequencies of 0.0‰–10.0‰, 10.0‰–20.0‰, 20.0‰–30.0‰, and over 30.0‰, respectively. The data is shown as a triplet codon (RSCU, relative synonymous codon usage), and high-frequency codons are underlined.
Mentions: A codon usage table was created by investigating all 138,002 codons (Table S1 in Supplementary file 1). With each codon, excepting three stop codons, GAG was most frequently presented, with the occurrence of 45.8‰, 2.8 times the average frequency. UCG was the lowest frequency codon (4.4‰) and another 14 codons also had low frequency (<10‰) (Figure 1). Measured by their codon frequencies, abundant and rare codons were defined as the 15 most abundant and 15 most rare codons in M. amblycephala. The overall GC content in the study is 0.494, but it varies among different codon positions, with the highest in GC3 (GC content of 3rd nucleotide in codons), at a value of 0.558, lowest in GC2 (GC content of 2nd nucleotide in codons), at a value of 0.389, and intermediate in GC1 (GC content of 1st nucleotide in codons), at a value of 0.534, which is consistent with the observations in other fishes (Table S2).

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.