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Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data

BACKGROUND: Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this...

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Autores principales: Feng, Chao, Xu, Chang-jie, Wang, Yue, Liu, Wen-li, Yin, Xue-ren, Li, Xian, Chen, Ming, Chen, Kun-song
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008310/
https://www.ncbi.nlm.nih.gov/pubmed/24160180
http://dx.doi.org/10.1186/1471-2164-14-732
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author Feng, Chao
Xu, Chang-jie
Wang, Yue
Liu, Wen-li
Yin, Xue-ren
Li, Xian
Chen, Ming
Chen, Kun-song
author_facet Feng, Chao
Xu, Chang-jie
Wang, Yue
Liu, Wen-li
Yin, Xue-ren
Li, Xian
Chen, Ming
Chen, Kun-song
author_sort Feng, Chao
collection PubMed
description BACKGROUND: Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species. RESULT: RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC(3s) (GC content of 3(rd) synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC(3s), especially in 'Molecular function’ category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. CONCLUSION: A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species.
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spelling pubmed-40083102014-05-03 Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data Feng, Chao Xu, Chang-jie Wang, Yue Liu, Wen-li Yin, Xue-ren Li, Xian Chen, Ming Chen, Kun-song BMC Genomics Research Article BACKGROUND: Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species. RESULT: RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC(3s) (GC content of 3(rd) synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC(3s), especially in 'Molecular function’ category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. CONCLUSION: A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species. BioMed Central 2013-10-25 /pmc/articles/PMC4008310/ /pubmed/24160180 http://dx.doi.org/10.1186/1471-2164-14-732 Text en Copyright © 2013 Feng et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Feng, Chao
Xu, Chang-jie
Wang, Yue
Liu, Wen-li
Yin, Xue-ren
Li, Xian
Chen, Ming
Chen, Kun-song
Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title_full Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title_fullStr Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title_full_unstemmed Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title_short Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
title_sort codon usage patterns in chinese bayberry (myrica rubra) based on rna-seq data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008310/
https://www.ncbi.nlm.nih.gov/pubmed/24160180
http://dx.doi.org/10.1186/1471-2164-14-732
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