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Int. J. Mol. Sci. 2015, 16(6), 11996-12013; doi:10.3390/ijms160611996

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

1
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
2
Lab of Biotecnología Genómica, Centro de Biotecnología Genómica, Instituto de Politécnico Nacional, Boulevard del Maestro S/N esq. Elías Piña, Col. Narciso Mendoza, Tamaulipas 88710, Mexico
*
Author to whom correspondence should be addressed.
Academic Editor: Jun Li
Received: 26 March 2015 / Accepted: 19 May 2015 / Published: 26 May 2015
(This article belongs to the Special Issue Fish Molecular Biology)
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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. View Full-Text
Keywords: RNA-Seq; Megalobrama amblycephala; codon usage; codon pairs; GC3 biology; methylation site; vertebrate evolution RNA-Seq; Megalobrama amblycephala; codon usage; codon pairs; GC3 biology; methylation site; vertebrate evolution
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Duan, X.; Yi, S.; Guo, X.; Wang, W. A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data. Int. J. Mol. Sci. 2015, 16, 11996-12013.

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