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.
Highlights
Blunt snout bream (Megalobrama amblycephala Yih, 1955), naturally distributed in the middle and lower reaches of the Yangtze River in China [1], has been one of the main aquaculture fish in China due to being a delicacy since the 1960s [2]
The study of codon usage based on the full length Open reading frame (ORF) sequences or genomes has been documented in a wide variety of organisms such as cyanobacteria [10], Caenorhabditis, Drosophila, Arabidopsis [11], Silene latifolia [12] and insects [13]
Codon usage analysis in M. amblycephala was based on 646 full-length ORF sequences after a filtering series from 100,477 unigenes, which were assembled and annotated in our previous work [4]
Summary
Blunt snout bream (Megalobrama amblycephala Yih, 1955), naturally distributed in the middle and lower reaches of the Yangtze River in China [1], has been one of the main aquaculture fish in China due to being a delicacy since the 1960s [2]. The wide variations in codon usage patterns of many organisms have provided clues to help understand genome evolution and some aspects of molecular biology [7,9,10,11,12]. The study of codon usage based on the full length ORF (open reading frame) sequences or genomes has been documented in a wide variety of organisms such as cyanobacteria [10], Caenorhabditis, Drosophila, Arabidopsis [11], Silene latifolia [12] and insects [13]. Large amounts of sequence data can be obtained through genome sequencing or RNA-Seq, providing an opportunity for the species-specific analysis of codon usage patterns in more non-model organisms. The results will improve our understanding of codon biology in M. amblycephala and fish evolution and will have potential applications for fish breeding
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