Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture
The fungal genus Puccinia, comprising of several menacing pathogens, has been a persistent peril to global agriculture. Genome sequencing of various members of Puccinia offers a scope to excavate their genomic riddles. The present study has been addressed at exploring the complex niceties of codo...
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| Формат: | Статья |
| Язык: | английский |
| Опубликовано: |
2025
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| Предметы: | |
| Online-ссылка: | https://repository.auw.edu.bd/handle/123456789/752 |
| _version_ | 1857448963233284096 |
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| author | Roy, Ayan |
| author_facet | Roy, Ayan |
| author_sort | Roy, Ayan |
| collection | institutional Repository |
| description | The fungal genus Puccinia, comprising of several menacing pathogens, has been
a persistent peril to global agriculture. Genome sequencing of various members
of Puccinia offers a scope to excavate their genomic riddles. The present study
has been addressed at exploring the complex niceties of codon and amino
acid usage patterns and subsequent elucidation of the determinants that drive
such behavior. Multivariate statistical analysis revealed a complex interplay of
natural selection for translation and compositional bias to be operational on the
codon usage patterns. Gene expression level was observed to be the most
competent factor governing codon usage behavior of the genus. In spite of
subtle AT richness of the genus, potential highly expressed gene sets were found
to preferentially employ GC rich optimal codons. Estimation of relative
dinucleotide abundance revealed preference toward the employment of GpA,
CpA, TpC, and TpG dinucleotides and restraint from using TpA dinucleotide
among the members of the genus. Extensive codon context analysis revealed
that codon pairs with GpA, CpA, TpC, and TpG dinucleotides were over‐
represented and codon pairs with TpA dinucleotide were extensively avoided at
the codon–codon (cP3–cA1) junctions. Amino acid usage signatures of the
genus were found to be influenced considerably by several imperative factors
like aromatic and hydrophobic character of the encoded gene products,
genomic compositional constraint, and gene expressivity. Detailed know‐how of
the potential highly expressed gene sets and associated optimal codons in the
genus promise to be informative for the scientific community engaged in
combating Puccinia pathogenesis. |
| format | Article |
| id | 123456789-752 |
| institution | Asian University for Women |
| language | English |
| publishDate | 2025 |
| record_format | dspace |
| spelling | 123456789-7522026-02-18T06:15:17Z Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture Roy, Ayan codon pair, correspondence analysis, dinucleotide frequency, Puccinia, relative amino acid usage, relative synonymous codon usage The fungal genus Puccinia, comprising of several menacing pathogens, has been a persistent peril to global agriculture. Genome sequencing of various members of Puccinia offers a scope to excavate their genomic riddles. The present study has been addressed at exploring the complex niceties of codon and amino acid usage patterns and subsequent elucidation of the determinants that drive such behavior. Multivariate statistical analysis revealed a complex interplay of natural selection for translation and compositional bias to be operational on the codon usage patterns. Gene expression level was observed to be the most competent factor governing codon usage behavior of the genus. In spite of subtle AT richness of the genus, potential highly expressed gene sets were found to preferentially employ GC rich optimal codons. Estimation of relative dinucleotide abundance revealed preference toward the employment of GpA, CpA, TpC, and TpG dinucleotides and restraint from using TpA dinucleotide among the members of the genus. Extensive codon context analysis revealed that codon pairs with GpA, CpA, TpC, and TpG dinucleotides were over‐ represented and codon pairs with TpA dinucleotide were extensively avoided at the codon–codon (cP3–cA1) junctions. Amino acid usage signatures of the genus were found to be influenced considerably by several imperative factors like aromatic and hydrophobic character of the encoded gene products, genomic compositional constraint, and gene expressivity. Detailed know‐how of the potential highly expressed gene sets and associated optimal codons in the genus promise to be informative for the scientific community engaged in combating Puccinia pathogenesis. 2025-07-22T06:00:30Z 2025-07-22T06:00:30Z 2018 Article https://repository.auw.edu.bd/handle/123456789/752 en application/pdf |
| spellingShingle | codon pair, correspondence analysis, dinucleotide frequency, Puccinia, relative amino acid usage, relative synonymous codon usage Roy, Ayan Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title | Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title_full | Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title_fullStr | Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title_full_unstemmed | Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title_short | Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture |
| title_sort | insights into the riddles of codon usage patterns and codon context signatures in fungal genus puccinia a persistent threat to global agriculture |
| topic | codon pair, correspondence analysis, dinucleotide frequency, Puccinia, relative amino acid usage, relative synonymous codon usage |
| url | https://repository.auw.edu.bd/handle/123456789/752 |
| work_keys_str_mv | AT royayan insightsintotheriddlesofcodonusagepatternsandcodoncontextsignaturesinfungalgenuspucciniaapersistentthreattoglobalagriculture |