Analysis of synonymous codon usage in FAD7 genes from different plant species

Ma, Qi; Li, C.; Wang, J.; Wang, Y.; Ding, Zhaotang

doi:10.4238/2015.february.13.20

Cited by 14 publications

(11 citation statements)

References 40 publications

(41 reference statements)

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“…Several cpSSRs identified in this study could be used for further genetic polymorphism detection of Phalaris species. The RSCU is thought to be influenced by a combination of natural selection, mutation, and genetic drift [33]. In this study, RSCU value was calculated using common coding genes of three Phalaris cp genomes, and our result indicated that the most and least abundant amino acids were leucine and cysteine, respectively, which is consistent with the previous study in the angiosperm cp genomes [34].…”

Section: Cpssrs and Rscusupporting

confidence: 88%

The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)

Xiong

Jia

2020

Plants

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There are 22 species in the Phalaris genera that distribute almost all over the temperate regions of the world. Among them, reed canary grass (Phalaris arundinacea, tetraploid and hexaploid) and hardinggrass (P. aquatica, tetraploid) have been long cultivated as forage grass and have received attention as bio-energy materials in recent years. We aimed to facilitate inter-species/ploidies comparisons, and to illuminate the degree of sequence variation within existing gene pools, chloroplast (cp) genomes of three Phalaris cytotypes (P. aquatica/4x, P. arundinacea/4x and P. arundinacea/6x) were sequenced and assembled. The result indicated that certain sequence variations existed between the cp genomes of P. arundinacea and P. aquatica. Several hotspot regions (atpI~atpH, trnT-UGU~ndhJ, rbcL~psaI, and ndhF~rpl32) were found, and variable genes (infA, psaI, psbK, etc.) were detected. SNPs (single nucleotide polymorphisms) and/or indels (insertions and deletions) were confirmed by the high Ka/Ks and Pi value. Furthermore, distribution and presence of cp simple sequence repeats (cpSSRs) were identified in the three Phalaris cp genomes, although little difference was found between hexaploid and tetraploid P. arundinacea, and no rearrangement was detected among the three Phalaris cp genomes. The evolutionary relationship and divergent time among these species were discussed. The RNA-seq revealed several differentially expressed genes (DEGs), among which psaA, psaB, and psbB related to leaf color were further verified by leaf color differences.

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Section: Cpssrs and Rscusupporting

confidence: 88%

The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)

Xiong

Jia

2020

Plants

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“…The notion of gene expression by CAI values was proposed for a long time ago, however, in recent years, the methods have been widely used to qualitatively assess high-level expression genes in prokaryote and eukaryote [38,39,40,41]. Fast development of the whole-genome analysis technologies, especially whole genome sequencing as well as proteomics has made it possible to compare computational data of codon usage and expression ability with experimental evidence.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Liu

Zhu

et al. 2016

IJMS

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Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.

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“…Nuclear genecoding regions of monocots are enriched in codons ending in C and G, whereas those of dicots have a higher proportion of codons ending in A and U [46]. A-and U-ending codons were predominant in seven different Citrus species and in FAD7 gene of dicots, whereas G-or C-ending codons were used for FAD7 of monocots [2,47].…”

Section: Genome Compositionmentioning

confidence: 99%

“…This universal phenomenon of usage of synonymous codons with different frequencies is termed as codon usage bias (CUB). CUB is widespread across species and serves as a code within the genetic code or the second genetic code [2,3]. Biased frequency of synonymous codons (CUB) varies not only among genomes, but also among functionally related genes and within a single gene [4].…”

Section: Introductionmentioning

confidence: 99%

Codon usage bias

2021

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Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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Analysis of synonymous codon usage in FAD7 genes from different plant species

Cited by 14 publications

References 40 publications

The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)

The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Codon usage bias

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