Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species

Yang, Chenkang; Zhao, Qi; Wang, Ying; Zhao, Jiajia; Liao, Qiao; Wu, Bangbang; Yan, Suxian; Zheng, Jun; Zheng, Xingwei

doi:10.3389/fgene.2021.732432

Cited by 12 publications

(9 citation statements)

References 57 publications

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“…Interestingly, this result is similar to GC3s content in gymnosperms such as Ginkgo biloba [31], Gnetifer Hypothesis [32], and most dicotyledons [32][33][34][35]. However, monocotyledons such as Triticum Aestivum [36],Zea Mays [37], Hordeum Vulgare [38], and Oryza Sativa [39] all showed high GC content and tended to end in G/C. RSCU analysis results reveal that similar to most higher plants [40], there is A or T use bias in the genome of C. panzhihuaensis.…”

Section: Discussionsupporting

confidence: 59%

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Jian¹,

Wang²,

Li³

et al. 2022

Preprint

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Codon use bias is an important characteristic in the process of genetic information transmission of species. With the publication of the genome of C. panzhihuaensis, it is of great significance to investigate the codon use bias for understanding the genetic evolution of this species and for molecular breeding. In this study, Perl language and CodonW 1.4.2 software was used to systematically analyze the coding gene sequences of the C. panzhihuaensis genome, obtain the characteristics of codon use, and identify the sources of variation affecting codon use. The results showed that GC3s content, GCall content, and ENC value were 46.75%, 47.67%, and 52.8 respectively. As the first seed plant, the GC3 content of Cycas is similar to that of most gymnosperms and most dicotyledons, but considerably different from that of monocotyledons.RSCU value was greater than 1, among which 21 codons ended in U or A. Enc-plot analysis, PR2-plot neutral plot analysis, and correlation coefficient analysis of Axis1 with GC3s and CAI revealed that the codon bias was mainly affected by natural selection, but also by mutation pressure and other factors. Thirty-one optimal codons of Cycas genes were screened. This research can provide a reference for the phylogeny and genome codon evolution of Cycas.

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Section: Discussionsupporting

confidence: 59%

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Jian¹,

Wang²,

Li³

et al. 2022

Preprint

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“…Codon use bias is mainly affected by many factors, including gene base composition, gene length, gene expression level, tRNA abundance, amino acid hydrophobicity, aromaticity, mutation, and selection, among which mutation and selection are the most important factors affecting codon use bias ( Trotta, 2013 ; Chen et al, 2014 ). Analyzing the codon bias characteristics and variations of different species is helpful to understanding the genetic structure and evolution trend of species ( Yang et al, 2021 ; Yu et al, 2021 ). Optimal codon analysis can also provide reference for the genetic expression of host genes.…”

Section: Discussionmentioning

confidence: 99%

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Luo

Sha

et al. 2023

Front. Microbiol.

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IntroductionCodon basis is a common and complex natural phenomenon observed in many kinds of organisms.MethodsIn the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.ResultsThe results showed that the codons of all Amanita species tended to end in A/T, demonstrating the preference of mitochondrial codons of Amanita species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of Amanita is 30.81, which is <35, demonstrating the strong codon preference of mitochondrial core PCGs of Amanita. The neutrality plot analysis and PR2-Bias plot analysis further demonstrated that natural selection plays an important role in Amanita codon bias. In addition, we obtained 5–10 optimal codons (ΔRSCU > 0.08 and RSCU > 1) in nine Amanita species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different Amanita species and found large variations between them.DiscussionThis study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.

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“…The overall result indicated that the composition of T is imperative in deciding the gene length; in other words, gene lengths affect the composition of T in genes associated with neurodegeneration. Yang et al (2021) linked a compositional parameter of the GC3 content to gene length, wherein genes shorter than 2,000 bp had a higher GC3 content than longer genes.…”

Section: Discussionmentioning

confidence: 99%

“…In animals, short genes show strong expression, whereas, in plants, long genes show strong expression (Ren et al, 2007). Similarly, composition and gene length are correlated; short genes (<2,000 bp) show an increased percentage of GC3 than do long genes (Yang et al, 2021). A significant positive correlation has been reported between gene length and synonymous CUB in Escherichia coli, whereas a negative correlation has been reported in Drosophila melanogaster and Saccharomyces cerevisiae, which depicts the strong bias toward longer genes to enhance translational efficiency because of selection pressure (Moriyama and Powell, 1998).…”

Section: Introductionmentioning

confidence: 99%

Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes

et al. 2022

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Codon usage analysis is a crucial part of molecular characterization and is used to determine the factors affecting the evolution of a gene. The length of a gene is an important parameter that affects the characteristics of the gene, such as codon usage, compositional parameters, and sometimes, its functions. In the present study, we investigated the association of various parameters related to codon usage with the length of genes. Gene expression is affected by nucleotide disproportion. In sixty genes related to neurodegenerative disorders, the G nucleotide was the most abundant and the T nucleotide was the least. The nucleotide T exhibited a significant association with the length of the gene at both the overall compositional level and the first and second codon positions. Codon usage bias (CUB) of these genes was affected by pyrimidine and keto skews. Gene length was found to be significantly correlated with codon bias in neurodegeneration associated genes. In gene segments with lengths below 1,200 bp and above 2,400 bp, CUB was positively associated with length. Relative synonymous CUB, which is another measure of CUB, showed that codons TTA, GTT, GTC, TCA, GGT, and GGA exhibited a positive association with length, whereas codons GTA, AGC, CGT, CGA, and GGG showed a negative association. GC-ending codons were preferred over AT-ending codons. Overall analysis indicated that the association between CUB and length varies depending on the segment size; however, CUB of 1,200–2,000 bp gene segments appeared not affected by gene length. In synopsis, analysis suggests that length of the genes correlates with various imperative molecular signatures including A/T nucleotide disproportion and codon choices. In the present study we additionally evaluated various molecular features and their correlation with different indices of codon usage, like the Codon Adaptation Index (CAI) and Relative Dynonymous Codon Usage (RSCU) of codons. We also considered the impact of gene fragment size on different molecular features in genes related to neurodegeneration. This analysis will aid our understanding of and in potentially modulating gene expression in cases of defective gene functioning in clinical settings.

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Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species

Cited by 12 publications

References 57 publications

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes

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