Analysis of codon usage bias of chloroplast genes in Oryza species

Chakraborty, Supriyo; Sophiarani, Yengkhom; Uddin, Arif

doi:10.1007/s00425-020-03470-7

Cited by 53 publications

(50 citation statements)

References 61 publications

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“…These significant correlations (p ≤ 0.001) indicated the critical role of mutation in shaping SCUB in the genomes of MCV-1 and MCV-2 but with varying intensities. Among the selected MCVs, in the seven genomes of MCV-1, slopes of regression lines were close to 1, revealing that mutational pressure is highly influential in determining SCUB (Figure 3a-g) [60,61], but the narrow distribution of GC3 could be due to the effect of some amount of selection. In the remaining genomes (two MCV-1 and all selected MC-2; Figure 3h-o), the scatter plots were widespread with relatively weaker correlations, and also the slopes of regression lines were ≤0.50.…”

Section: Relative Magnitude Of Selection Versus Mutationmentioning

confidence: 88%

“…Correspondence analyses (CA) was performed on 59 synonymous codons (excluding ATG for Met, TGG for Trp, termination codons TAA, TAG and TGA) by assuming each coding sequence as a 59-dimensional vector with each dimension identical to RSCU value of a codon [61,95] for delineating SCU variations across the genes of MCV genomes. The relative importance of each codon over each orthogonal axis is represented by eigen value [96].…”

Section: Correspondence Analysismentioning

confidence: 99%

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Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Nair¹,

Mohan

Rudramurthy

et al. 2021

Pathogens

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Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.

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Section: Relative Magnitude Of Selection Versus Mutationmentioning

confidence: 88%

Section: Correspondence Analysismentioning

confidence: 99%

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Nair¹,

Mohan

Rudramurthy

et al. 2021

Pathogens

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“…The codon usage pattern reflects the evolution and mutation of species or genes and also plays an important role in gene expression level and functional differentiation [33,34]. By analyzing the GA20ox, C19GA20x, and C20GA2ox subgroup genes in 21 species (approximately 391 sequences; Table S2), we constructed relatively systematic codon usage patterns in the gibberellin oxidase gene family.…”

Section: Codon Usage Pattern Analysis In Gaox Genesmentioning

confidence: 99%

Gibberellin Oxidase Gene Family in L. chinense: Genome-Wide Identification and Gene Expression Analysis

Wang

Hao

et al. 2021

IJMS

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GAox is a key enzyme for the transformation of gibberellins, and belongs to the 2-ketoglutarate dependent dioxygenase gene family (2ODD). However, a systematic analysis of GAox in the angiosperm L. chinense has not yet been reported. Here, we identified all LcGAox gene family members in L. chinense, which were classified into the three subgroups of GA20ox, C19GA2ox, and C20GA2ox. Comparison of the gene structure, conserve motifs, phylogenetic relationships, and syntenic relationships of gibberellin oxidase gene families in different species indicated that the gene functional differences may be due to the partial deletion of their domains during evolution. Furthermore, evidence for purifying selection was detected between orthologous GAox genes in rice, grape, Arabidopsis, and L. chinense. Analysis of the codon usage patterns showed that mutation pressure and natural selection might have induced codon usage bias in angiosperms; however, the LcGAox genes in mosses, lycophytes, and ambarella plants exhibited no obvious codon usage preference. These results suggested that the gibberellin oxidase genes were more primitive. The gene expression pattern was analyzed in different organs subjected to multiple abiotic stresses, including GA, abscisic acid (ABA), and chlormequat (CCC) treatment, by RNA-seq and qRT-PCR, and the stress- and phytohormone-responsive cis-elements were counted. The results showed that the synthesis and decomposition of GA were regulated by different LcGAox genes in the vegetative and reproductive organs of L. chinense, and only LcGA2ox1,4, and 7 responded to the NaCl, polyethylene glycol, 4 °C, GA, ABA, and CCC treatment in the roots, stems, and leaves of seedlings at different time periods, revealing the potential role of LcGAox in stress resistance.

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“…Codons serve an essential function in transmitting genetic information [21]. This information is passed along from DNA to RNA to protein using codons, which are sets of three nucleotides.…”

Section: Introductionmentioning

confidence: 99%

“…Based on our existing knowledge of the cp genome, genetic engineering using CUB can greatly enhance plant genome in a way that maximizes pharmacological bene t [29]. Till now, studies have examined cp genome CUB in various plants, including Drynaria [30], Panicum species [31], and Oryza species [21]. However, thus far, there have been no reports of CUB in Lepidium Genomic studies, including nuclear and organelle DNA, can enhance our understanding of the origin of medicinal plants.…”

Section: Introductionmentioning

confidence: 99%

A Comparative Study of the Chloroplast Genomes of Five Lepidium Medicinal Plants

Zhou¹,

Chen²,

Ming-yuan³

et al. 2021

Preprint

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Background Herb genomics is a rapidly developing field of medicinal plant research and development. Plant genomic studies demonstrate the unique advantage of employing plants in medicinal therapy. The genus Lepidium falls under the Brassicaceae family and it includes crucial medicinal plants. Herein, we sequenced the complete chloroplast (cp) genomes of Lepidium apetalum (LA) and Lepidium perfoliatum (LP) and assessed their genetic profiles against the reported profiles of Lepidium sativum (LS), Lepidium meyenii (LM), and Lepidium virginicum (LV). Results In particular, we examined genomic arrangement, gene number, type, and repeat sequences. Based on our annotation data, both LA and LP possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA) genes. Our repeat analyses revealed that LA harbored 20 forward repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas LP had 15 forward repeats, 20 palindrome repeats,4 reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium cp genomes and a remarkably high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments, particularly in the intergenic regions of the trnK-atpA, trnC-psbC, trnT-rbcL, ndhF-ndhH, ycf1-trnR, accD, ccsA, matK, ndhF, rpoB, rpoC2, and ycf1 genes. Moreover, following codon usage analysis, we observed that codon 14 was the most frequently used codon in the Lepidium CDS. In addition, correlation investigations revealed that the ENC (the effective number of codon) content was strongly associated with GC3, GC3s, and N. Conclusion Based on these data, LA and LP originate from very similar genetic backgrounds. Furthermore, neutrality, ENC, and PR2-plots analyses demonstrated that the CUB (the codon usage bias) of Lepidium cp genome was strongly influenced by mutation and natural selection. Our analysis of the cp genomic sequences of LA and LP will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.

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Analysis of codon usage bias of chloroplast genes in Oryza species

Cited by 53 publications

References 61 publications

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Gibberellin Oxidase Gene Family in L. chinense: Genome-Wide Identification and Gene Expression Analysis

A Comparative Study of the Chloroplast Genomes of Five Lepidium Medicinal Plants

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