Trends and Anomalies in Nucleotide Selection at Three Codon Sites of Microbials Genes an In Silico Analysis

Das, Sabyasachi (2006) Trends and Anomalies in Nucleotide Selection at Three Codon Sites of Microbials Genes an In Silico Analysis. PhD thesis, Jadavpur University.

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    Supervisors

    SupervisorsEmail
    Dutta, Chitra

    Abstract

    Compositional heterogeneity is an intrinsic feature of genome sequences. Inhomogeneous patterns of base composition are often observed along a genome sequence, which may reflect important aspects of genomic organization: (1) formation of compartments (i.e., AT- or GC rich traits of the genome, due to neutral or selective events) (Sueoka 1988), (2) acquisition of new genetic materials from outside (e.g., horizontal genes transfer (Syvanen 1994; Ochman et al. 2005) and (3 insertion/deletion events (Andersson and Andersson 1999). In all cases,this behavior interferes with the normal divergent pattern of vertical evolution and complicates the phylogenetic analysis of organisms and, even more so, the measurements of their evolutionary distances. The base composition of DNA varies appreciably from organism to organism. In bacteria, the mean genomic G+C-content ranges from 25 to 75 per cent (Belozersky and Spirin 1958). In general, intra-genomic divergence in GC-bias is not very large in microorganisms. However, the presence of distinct regions having different %GC values has been described in several microbial genomes. In some species, a region with GC content higher than in the remaining genome has been found: for example, in the rRNA operons of Aquifex aeolicus and Mycoplasma genitalium. Other organisms have a lower GC value in some regions: for example, in genes for polysaccharide production of the archaeon Methanobacterium jannaschi [probably a mark of a lateral transfer event (Bult et al. 1996), and in Bacillus subtilis, where many (A + T)-rich islands are present, probably a remnant of bacteriophage lysogens or other inserted elements.

    Item Type: Thesis (PhD)
    URI: http://www.eprints.iicb.res.in/id/eprint/1592
    Subjects: Structural Biology & Bioinformatics
    Divisions: Indian Institute of Chemical Biology
    Depositing User: Mr Santanu Sadhukhan
    Date Deposited: 06 Aug 2012 11:59
    Last Modified: 06 Aug 2012 11:59
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