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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

Logo analyses of start and stop codon contexts and the codon bias following AUG in M. amblycephala. (A,B) Logo analyses of 18 nucleotides around the start codon (A) and stop codons (B). The vertical axis represents the conservation at a certain position (measured in bits). The horizontal axis represents the nucleotide position around the start codon or stop codons. For mapping convenience, the start and stop codons were removed from the resultant map; (C,D) Distribution of the ratio of observed frequency to expected frequency in different types of codons following the start codon AUG (C) and non-start internal codon AUG (D); The X axis shows the types of codons, where n represent A, G, C or U; (E,F) The relationship between observed frequency and expected frequency of 61 codons following the start codon AUG (E) and non-start internal codon AUG (F). The red, green and black spots represent the preferred codons, avoided codons and unbiased codons, respectively. The lowest p-value was set to 1 × 10−10.
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ijms-16-11996-f004: Logo analyses of start and stop codon contexts and the codon bias following AUG in M. amblycephala. (A,B) Logo analyses of 18 nucleotides around the start codon (A) and stop codons (B). The vertical axis represents the conservation at a certain position (measured in bits). The horizontal axis represents the nucleotide position around the start codon or stop codons. For mapping convenience, the start and stop codons were removed from the resultant map; (C,D) Distribution of the ratio of observed frequency to expected frequency in different types of codons following the start codon AUG (C) and non-start internal codon AUG (D); The X axis shows the types of codons, where n represent A, G, C or U; (E,F) The relationship between observed frequency and expected frequency of 61 codons following the start codon AUG (E) and non-start internal codon AUG (F). The red, green and black spots represent the preferred codons, avoided codons and unbiased codons, respectively. The lowest p-value was set to 1 × 10−10.

Mentions: Moreover, the heterogeneity close to the 5ʹ-region and 3ʹ-region in M. amblycephala may shape some preferential flanking sequence characters around start and stop codons (Figure 4A,B). Further analysis showed the preferred nucleotide “G” (Figure 4C) following the start codon AUG, together with “A” just preceding three positions of the start codon AUG, in accordance with the Kozak sequence for identification of the translation start site [24]. The preferential motif would be of species-specific significance in enhancing start codon recognition and translation efficiency [25], which was verified in Danio rerio [26]. Meanwhile, 5 preferred and 7 avoided codons were observed for the codon following the start codon AUG (Figure 4E). In contrast, there was no bias observed in the nucleotides or codons following internal AUG codons of genes (Figure 4D,F). This phenomenon confirmed that the bias was related to position-dependent rather than the bias codon following AUG itself. As for the termination codons, a certain relationship with stop codons bias was presented (Figure S1C–E). The maintained bias in stop codon contexts may promote RF (polypeptide release factor) bond efficiency with mRNA to affect translation termination [27,28,29,30].


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)

Logo analyses of start and stop codon contexts and the codon bias following AUG in M. amblycephala. (A,B) Logo analyses of 18 nucleotides around the start codon (A) and stop codons (B). The vertical axis represents the conservation at a certain position (measured in bits). The horizontal axis represents the nucleotide position around the start codon or stop codons. For mapping convenience, the start and stop codons were removed from the resultant map; (C,D) Distribution of the ratio of observed frequency to expected frequency in different types of codons following the start codon AUG (C) and non-start internal codon AUG (D); The X axis shows the types of codons, where n represent A, G, C or U; (E,F) The relationship between observed frequency and expected frequency of 61 codons following the start codon AUG (E) and non-start internal codon AUG (F). The red, green and black spots represent the preferred codons, avoided codons and unbiased codons, respectively. The lowest p-value was set to 1 × 10−10.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-11996-f004: Logo analyses of start and stop codon contexts and the codon bias following AUG in M. amblycephala. (A,B) Logo analyses of 18 nucleotides around the start codon (A) and stop codons (B). The vertical axis represents the conservation at a certain position (measured in bits). The horizontal axis represents the nucleotide position around the start codon or stop codons. For mapping convenience, the start and stop codons were removed from the resultant map; (C,D) Distribution of the ratio of observed frequency to expected frequency in different types of codons following the start codon AUG (C) and non-start internal codon AUG (D); The X axis shows the types of codons, where n represent A, G, C or U; (E,F) The relationship between observed frequency and expected frequency of 61 codons following the start codon AUG (E) and non-start internal codon AUG (F). The red, green and black spots represent the preferred codons, avoided codons and unbiased codons, respectively. The lowest p-value was set to 1 × 10−10.
Mentions: Moreover, the heterogeneity close to the 5ʹ-region and 3ʹ-region in M. amblycephala may shape some preferential flanking sequence characters around start and stop codons (Figure 4A,B). Further analysis showed the preferred nucleotide “G” (Figure 4C) following the start codon AUG, together with “A” just preceding three positions of the start codon AUG, in accordance with the Kozak sequence for identification of the translation start site [24]. The preferential motif would be of species-specific significance in enhancing start codon recognition and translation efficiency [25], which was verified in Danio rerio [26]. Meanwhile, 5 preferred and 7 avoided codons were observed for the codon following the start codon AUG (Figure 4E). In contrast, there was no bias observed in the nucleotides or codons following internal AUG codons of genes (Figure 4D,F). This phenomenon confirmed that the bias was related to position-dependent rather than the bias codon following AUG itself. As for the termination codons, a certain relationship with stop codons bias was presented (Figure S1C–E). The maintained bias in stop codon contexts may promote RF (polypeptide release factor) bond efficiency with mRNA to affect translation termination [27,28,29,30].

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