A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data

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.

Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation

“…Earlier study also found positive correlation between GC3, overall GC and SCUO (Duan et al, 2015). Wan et al (Wan et al, 2004) found similar results in unicellular genome.…”

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

“…50 The genes that possess higher GC3 are usually more susceptible to cellular methylation and finally lead to a greater probability of mutation compared with the genes with lower GC3. 51 Duan et al (2015) reported that GC composition at third codon position (GC3) was higher than GC composition at the first codon position (GC1) in fishes and mammals, while lower in amphibians, reptiles, and birds with the exception of Taeniopygia guttata. 52 Two evolutionary forces, namely mutation pressure and natural selection, are considered as the origin of CUB in genes.…”

“…51 Duan et al (2015) reported that GC composition at third codon position (GC3) was higher than GC composition at the first codon position (GC1) in fishes and mammals, while lower in amphibians, reptiles, and birds with the exception of Taeniopygia guttata. 52 Two evolutionary forces, namely mutation pressure and natural selection, are considered as the origin of CUB in genes. But our present study showed highly remarkable correlation between overall nucleotide composition of A, T, G, C, and GC contents and the relative nucleotide composition at third codon position, which revealed that both the two evolutionary forces might influence the CUB in ATP6 and ATP8 genes among the diverse species of fishes, birds, and mammals.…”

Analysis of codon usage patterns inMorus notabilisbased on genome and transcriptome data

“…In M. notabilis, the NCG codons had low RSCU values (GCG 0.58,UCG 0.696,ACG 0.62,CCG 0.732). We used the previously reported parameter XCG: XCC to evaluate CpG suppression (Duan et al 2015;Gonzalezibeas et al 2007;Sterky et al 2004), and found that CpG suppression was weakest in M. notabilis (with the exception of the strawberry cultivar Fragaria × ananassa) compared with the other Rosales species (Table S1 in Supplementary file 2), implying a high mutation rate and low methylation level in M. notabilis. This result also indicated high evolutionary rates in internal and last exons (Chuang et al 2012;Keller and Yi 2014;Takuno and Gaut 2012), but the data are not sufficient to fully explain why M. notabilis evolved about three times faster than several other Rosales species (He et al 2013).…”

“…Contextual bias has been studied in multicellular organism Megalobrama amblycephala (Duan et al 2015), and contextual bias was also observed in M.…”