Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of

Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of

Oncidium Gower Ramsey is a fascinating and important ornamental flower in floral industry. In this research, the complete nucleotide sequence of the chloroplast genome in Oncidium Gower Ramsey was studied, then analyzed using Codonw software. Correspondence analysis and method of effective number of...

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Main Authors: Chen Xu, Xiaoning Cai, Quanzhan Chen, Hongxia Zhou, Yao Cai, Ailing Ben
Format: Article
Language:English
Published: SAGE Publishing 2011-01-01
Series:Evolutionary Bioinformatics
Online Access:https://doi.org/10.4137/EBO.S8092
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spelling doaj-0b9f743192be45ce87d1a0a01decd23f2020-11-25T03:17:32ZengSAGE PublishingEvolutionary Bioinformatics1176-93432011-01-01710.4137/EBO.S8092Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Chen Xu0Xiaoning Cai1Quanzhan Chen2Hongxia Zhou3Yao Cai4Ailing Ben5School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.School of Biochemical and Environmental Engineering, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China.Oncidium Gower Ramsey is a fascinating and important ornamental flower in floral industry. In this research, the complete nucleotide sequence of the chloroplast genome in Oncidium Gower Ramsey was studied, then analyzed using Codonw software. Correspondence analysis and method of effective number of codon as Nc-plot were conducted to analyze synonymous codon usage. According to the corresponding analysis, codon bias in the chloroplast genome of Oncidium Gower Ramsey is related to their gene length, mutation bias, gene hydropathy level of each protein, gene function and selection or gene expression only subtly affect codon usage. This study will provide insights into the molecular evolution study and high-level transgene expression.https://doi.org/10.4137/EBO.S8092
collection DOAJ
language English
format Article
sources DOAJ
author Chen Xu
Xiaoning Cai
Quanzhan Chen
Hongxia Zhou
Yao Cai
Ailing Ben
spellingShingle Chen Xu
Xiaoning Cai
Quanzhan Chen
Hongxia Zhou
Yao Cai
Ailing Ben
Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
Evolutionary Bioinformatics
author_facet Chen Xu
Xiaoning Cai
Quanzhan Chen
Hongxia Zhou
Yao Cai
Ailing Ben
author_sort Chen Xu
title Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
title_short Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
title_full Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
title_fullStr Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
title_full_unstemmed Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of
title_sort factors affecting synonymous codon usage bias in chloroplast genome of
publisher SAGE Publishing
series Evolutionary Bioinformatics
issn 1176-9343
publishDate 2011-01-01
description Oncidium Gower Ramsey is a fascinating and important ornamental flower in floral industry. In this research, the complete nucleotide sequence of the chloroplast genome in Oncidium Gower Ramsey was studied, then analyzed using Codonw software. Correspondence analysis and method of effective number of codon as Nc-plot were conducted to analyze synonymous codon usage. According to the corresponding analysis, codon bias in the chloroplast genome of Oncidium Gower Ramsey is related to their gene length, mutation bias, gene hydropathy level of each protein, gene function and selection or gene expression only subtly affect codon usage. This study will provide insights into the molecular evolution study and high-level transgene expression.
url https://doi.org/10.4137/EBO.S8092
work_keys_str_mv AT chenxu factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
AT xiaoningcai factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
AT quanzhanchen factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
AT hongxiazhou factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
AT yaocai factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
AT ailingben factorsaffectingsynonymouscodonusagebiasinchloroplastgenomeof
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