TY - JOUR
T1 - A comprehensive analysis of codon usage patterns in blunt snout bream (Megalobrama amblycephala) based on RNA-Seq data
AU - Duan, Xiaoke
AU - Yi, Shaokui
AU - Guo, Xianwu
AU - Wang, Weimin
N1 - Publisher Copyright:
© 2015 by the authors; licensee MDPI, Basel, Switzerland.
PY - 2015/5/26
Y1 - 2015/5/26
N2 - 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.
AB - 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.
KW - Codon pairs
KW - Codon usage
KW - GC biology
KW - Megalobrama amblycephala
KW - Methylation site
KW - RNA-Seq
KW - Vertebrate evolution
UR - http://www.scopus.com/inward/record.url?scp=84930657301&partnerID=8YFLogxK
U2 - 10.3390/ijms160611996
DO - 10.3390/ijms160611996
M3 - Artículo
SN - 1661-6596
VL - 16
SP - 11996
EP - 12013
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 6
ER -