Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens

Gupta, Suruchi; Singh, Ravail

doi:10.1007/s00438-021-01808-8

Cited by 13 publications

(12 citation statements)

References 35 publications

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“…The same was also evident in the case of A. alternata [68]. Further, the dual effect of natural selection and mutation pressure on the dispersal of codons from the centre of the PR2 plot was confirmed in the TP3 gene family [38], Zingiber officinale, and its associated fungal pathogens [79].…”

Section: Pr2 Plot Analysismentioning

confidence: 53%

“…An exception to the current observation was S. cerevisiae, which favoured AT-rich codons rather than GC, and showed a positive correlation with AT and AT3. Perseverance of GC-rich codons facilitates pathogen invasion in the host system by promoting gene expression, and this richness of G and C is common in fungal genomes [46,79].…”

Section: Codon Adaptation Index (Cai)mentioning

confidence: 99%

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Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Bansal

Mallikarjuna

Balamurugan

et al. 2022

JoF

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Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host–pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host–pathogen interactions through genome editing and functional genomics tools

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Section: Pr2 Plot Analysismentioning

confidence: 53%

Section: Codon Adaptation Index (Cai)mentioning

confidence: 99%

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Bansal

Mallikarjuna

Balamurugan

et al. 2022

JoF

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“…The amino acid composition is a crucial element in determining an organism's physiological function (Gupta and Singh 2021a). We observed leucine was found to be the most abundant amino acid in C. sativus followed by serine and glycine.…”

Section: Discussionmentioning

confidence: 74%

“…Among them, mutational pressure and natural selection are the two elementary evolutionary forces that principally affects the CUB. In fact, the outcome of the balance between these two important factors shape the codon usage pattern operative in genomes of different organisms (Gupta and Singh 2021a). Different softwares and online tools are used to measure CUB related indices (ENC, CAI, CBI, RSCU) and plots (ENC plot, neutrality plot, parity plot, Correspondence plot) etc.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the role of codon usage bias on gene expression and pathogen colonization in Crocus sativus

Nisa

Gupta

Waqas

et al. 2022

Preprint

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Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explicates the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with ENC < 50 had low FPKM value while low codon bias group (ENC > 50) possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus. The non-significant MELP and ENC correlation analysis suggested that expression of genes might not be associated with CUB. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping CUB. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all three species. In addition, the role of CUB regarding the predilection of fungal pathogens Aspergillus fumigatus and Fusarium oxysporum towards host plant C. sativus has also been expounded. We found a similar trend of codon usage pattern operative in plant and fungal pathogens as both the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus. Overall, different CUB indices reflected a weak codon bias in the C. sativus, F. oxysporum and A. fumigatus genome.

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“…Nevertheless, some differences between conserved and non-conserved ORFs were observed in the differential use of synonymous codons, namely codon usage bias (CUB). The codon bias has been reported in many organisms (Duret, 2002;Sharp et al, 2005;Xiang et al, 2015;Gupta and Singh, 2021) including mitochondrial genomes (Wei et al, 2014;Yildiz and Ozkilinc, 2021). Highly-expressed genes exhibit a strong bias to conserve their translational efficiency.…”

Section: Discussionmentioning

confidence: 99%

The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family

Valenti

Degradi

Kunova

et al. 2022

Front. Fungal Biol.

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Ciborinia camelliae is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus Camellia, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of Ciborinia camellia is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (rps3) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of C. camelliae. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.

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Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens

Cited by 13 publications

References 35 publications

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Deciphering the role of codon usage bias on gene expression and pathogen colonization in Crocus sativus

The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family

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