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.


Gene ontology (GO) classifications for three GC3 levels in M. amblycephala. * indicates, in a particular GO category at the 5% level, a significantly higher percentage of genes in high GC3 groups than low GC3 groups, while the percentage of mid GC3 groups is intermediate; ^ represents an opposite situation.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f006: Gene ontology (GO) classifications for three GC3 levels in M. amblycephala. * indicates, in a particular GO category at the 5% level, a significantly higher percentage of genes in high GC3 groups than low GC3 groups, while the percentage of mid GC3 groups is intermediate; ^ represents an opposite situation.

Mentions: For a better understanding of the influence of GC3 on gene properties in M. amblycephala, all the ORFs were almost equally separated into three groups according to GC3 value, respectively containing 215, 216 and 215 sequences, for gene ontology (GO) classification analysis. Six GO categories with significant difference among three groups were observed (Figure 6). Five out of six categories, the exception being the “catalytic activity” category, showed positive correlation between gene representation and GC3 value. It was further found that GC3-rich genes tend to be more enriched in dinucleotide CG (Figure S2B,C), indicating more targets to be methylated [35] for fine-tuning of transcriptional regulation [36]. In contrast, there is no significant difference in the relative abundance of trinucleotide CWG, where W stands for A or T, between the two classes of genes (Figure S2D). The observations support the earlier suggestion that CG and CWG methylation may serve different biological functions [37] in GC3-rich genes from in GC3-poor genes. The above revealed that GC3 bias may be a major factor in driving codon usage bias among genes and relates to gene function and methylation regulation in M. amblycephala.


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)

Gene ontology (GO) classifications for three GC3 levels in M. amblycephala. * indicates, in a particular GO category at the 5% level, a significantly higher percentage of genes in high GC3 groups than low GC3 groups, while the percentage of mid GC3 groups is intermediate; ^ represents an opposite situation.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f006: Gene ontology (GO) classifications for three GC3 levels in M. amblycephala. * indicates, in a particular GO category at the 5% level, a significantly higher percentage of genes in high GC3 groups than low GC3 groups, while the percentage of mid GC3 groups is intermediate; ^ represents an opposite situation.
Mentions: For a better understanding of the influence of GC3 on gene properties in M. amblycephala, all the ORFs were almost equally separated into three groups according to GC3 value, respectively containing 215, 216 and 215 sequences, for gene ontology (GO) classification analysis. Six GO categories with significant difference among three groups were observed (Figure 6). Five out of six categories, the exception being the “catalytic activity” category, showed positive correlation between gene representation and GC3 value. It was further found that GC3-rich genes tend to be more enriched in dinucleotide CG (Figure S2B,C), indicating more targets to be methylated [35] for fine-tuning of transcriptional regulation [36]. In contrast, there is no significant difference in the relative abundance of trinucleotide CWG, where W stands for A or T, between the two classes of genes (Figure S2D). The observations support the earlier suggestion that CG and CWG methylation may serve different biological functions [37] in GC3-rich genes from in GC3-poor genes. The above revealed that GC3 bias may be a major factor in driving codon usage bias among genes and relates to gene function and methylation regulation in M. amblycephala.

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.