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Sequence analysis of 16S rRNA gene inRhinosporidium seeberi shows similarity to plant chloroplast DNA.

ABSTRACT:

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Identity of causative agent of rhinosporidiosis (Rhinosporidium seeberi) has been controversial since the disease was described in 1900. Extensive sequence alignments and phylogenetic analyses of 16S rRNA gene detected recently by us in R. seeberi , revealed 99% similarity with 16S rDNA in chloroplasts of flowering plants. Study demonstrates R. seeberi is a pigmented prokaryote displaying some characteristics of cyanobacteria, and contains 16S rDNA present in chloroplasts of all groups of land plants. This study and our recent publication of 2006 are the first molecular studies using purified organismal DNA extracted from R. seeberi free of infected tissue.

Abbreviations

RB - Round body.

SUBMITTER: Ahluwalia KB

PROVIDER: S-EPMC3040483 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Sequence analysis of 16S rRNA gene inRhinosporidium seeberi shows similarity to plant chloroplast DNA.

Ahluwalia Karvita B KB Dhaulakhandi Dhara B DB Garg Lalit C LC

Bioinformation 20100920 3

<h4>Unlabelled</h4>Identity of causative agent of rhinosporidiosis (Rhinosporidium seeberi) has been controversial since the disease was described in 1900. Extensive sequence alignments and phylogenetic analyses of 16S rRNA gene detected recently by us in R. seeberi , revealed 99% similarity with 16S rDNA in chloroplasts of flowering plants. Study demonstrates R. seeberi is a pigmented prokaryote displaying some characteristics of cyanobacteria, and contains 16S rDNA present in chloroplasts of a ...[more]

PMID: 21364787

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Project description:BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM) of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52%) corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra-species variability.

Dataset Information

Sequence analysis of 16S rRNA gene inRhinosporidium seeberi shows similarity to plant chloroplast DNA.

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Abbreviations

Publications

Sequence analysis of 16S rRNA gene inRhinosporidium seeberi shows similarity to plant chloroplast DNA.

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