Article: A comparative-based phylogenetic study in the evolution of 16S rRNA and rad a genes in Archaea Journal: International Journal of Data Mining and Bioinformatics (IJDMB) 2012 Vol.6 No.4 pp.396 - 405 Abstract: Archaea are ubiquitous in their presence and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the earth. The identification of archaeal genomic signatures elucidates us a measure of distinctiveness of Archaea as a coherent group, although these signatures can differ according to the degree of stringency. The 16S rRNA and the Rad A genes are highly conserved in living organisms and are very useful for the phylogenetic analysis. Phylogenetic trees are constructed using the Molecular Evolutionary Genetics Analysis (MEGA) tool by Neighbour Joining (NJ) method and repeated bootstrapping for 5000 times was performed. The two trees were then compared using the Compare2trees and statistically analysed using the MEGA tool. The two phylogenetic trees show a similarity of 54.9%. In both the trees, the taxon Thaumarchaeota shows a high level of variance. The species Cenarchaeum symbiosum A shows a high level of similarity with the sequences of higher organisms (Euryarcheota-eukaryota), which shows that it has branched away to higher organisms from a closely related Protozoa, Eubacteria ancestor. Inderscience Publishers - linking academia, business and industry through research

Title: A comparative-based phylogenetic study in the evolution of 16S rRNA and rad a genes in Archaea

Authors: K.R.S. Sambasiva Rao; D. Srinivasa Rao

Addresses: Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 510, AP, India ' Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 510, AP, India

Abstract: Archaea are ubiquitous in their presence and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the earth. The identification of archaeal genomic signatures elucidates us a measure of distinctiveness of Archaea as a coherent group, although these signatures can differ according to the degree of stringency. The 16S rRNA and the Rad A genes are highly conserved in living organisms and are very useful for the phylogenetic analysis. Phylogenetic trees are constructed using the Molecular Evolutionary Genetics Analysis (MEGA) tool by Neighbour Joining (NJ) method and repeated bootstrapping for 5000 times was performed. The two trees were then compared using the Compare2trees and statistically analysed using the MEGA tool. The two phylogenetic trees show a similarity of 54.9%. In both the trees, the taxon Thaumarchaeota shows a high level of variance. The species Cenarchaeum symbiosum A shows a high level of similarity with the sequences of higher organisms (Euryarcheota-eukaryota), which shows that it has branched away to higher organisms from a closely related Protozoa, Eubacteria ancestor.

Keywords: Archaea; archaeal genomic signatures; NJ method; bootstraping; Thaumarchaeota; 16S rRNA genes; rad A genes; phylogenetic trees; molecular evolutionary genetics; neighbour joining; genetic evolution; protozoa.

DOI: 10.1504/IJDMB.2012.049277

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.4, pp.396 - 405

Received: 31 May 2010
Accepted: 06 Nov 2010
Published online: 17 Dec 2014 *

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Title: A comparative-based phylogenetic study in the evolution of 16S rRNA and rad a genes in Archaea

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