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

Abstract

BackgroundCodon 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.ResultRNA-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 GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, 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.ConclusionA 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.

Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending

“…There are still many debates on the detailed classification of gymnosperms, and G. biloba plays a very important role in this classification system due to its unique characteristics, such as the rare broad leaves and diclinism, which are very different to other gymnosperms19. Although studies on codon usage bias have been widely studied in Caenorhabditis 20, Arabidopsis 21, Populus 22, Myrica rubra 23 and Bombyx mori 24—no systematic research on codon usage patterns and the related base composition (GC3 contents) together with functional classification in gymnosperms has been reported. In our previous study, we performed RNA-Seq sequencing of G. biloba and the data (accession number: SRP062414) was made publicly available25.…”

Adaptation of Borrelia burgdorferi to its natural hosts by synonymous codon and amino acid usage

“…The first 50 codons (excluding the start codon) of all genes we obtained via manual edition were termed cod_2 to cod_50. Codons with the same name were mixed and recorded in FASTA format, after which the new rearranged sequences were structured and calculated using the CAI index formula to represent the codon distribution at different positions . Additionally, to analyze the synonymous codon usage bias in the translation initiation region (the 2nd to 10th codon positions), which comprises the aligned codons located at the 2nd codon position, 3rd codon position, 4th codon position, …, 8th codon position, 9th codon position, and 10th codon position of ORFs in the B. burgdorferi genome, we referred to the formula for synonymous codon usage bias in the specific coding region and established a simple formula for estimating the synonymous codon usage bias of each codon position in the translation initiation region.…”

“…The first 50 codons (excluding the start codon) of all genes we obtained via manual edition were termed cod_2 to cod_50. Codons with the same name were mixed and recorded in FASTA format, after which the new rearranged sequences were structured and calculated using the CAI index formula to represent the codon distribution at different positions [41]. Additionally, to analyze the synonymous codon usage bias in the translation initiation region (the 2nd to 10th codon positions), which comprises the aligned codons located at the 2nd codon position, 3rd codon position, 4th codon position, .…”

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli

“…One http://dx.doi.org/10.1016/j.enzmictec.2015.04.008 0141-0229/© 2015 Elsevier Inc. All rights reserved. approach is to identify highly expressed genes using microarray or RNA-Seq global transcriptome data [16,17]. This is based on the argument that mRNA and protein levels are well correlated in microbial hosts [7], though the correlation is weaker for higher eukaryotes [18].…”