https://repository.auw.edu.bd/handle/123456789/680 2026-06-09T23:47:53Z https://repository.auw.edu.bd/handle/123456789/752 Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture Roy, Ayan 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. 2018-01-01T00:00:00Z https://repository.auw.edu.bd/handle/123456789/751 Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities Roy, Ayan The present study has been aimed to the com- parative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phyloge- netic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydro- phobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypoth- esis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebac- terium. The study reveals close relationship between non- pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism. 2018-01-01T00:00:00Z https://repository.auw.edu.bd/handle/123456789/750 Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex Roy, Ayan Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic spe- cies, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close re- lationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature. 2018-01-01T00:00:00Z