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16S rRNA based identification of Aeromonas sp. kumar by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar

P. Kumar¹, C. M. Ramakritinan¹ & A. K. Kumaraguru¹

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1. Centre for Marine and Coastal Studies, Madurai Kamaraj University

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Document Type:

Manuscript

Date:

Received 28 October 2009 02:02 UTC; Posted 28 October 2009

Subjects:

Ecology, Microbiology, Bioinformatics

Tags:

• Red tide Bloom
• PCR
• Neighbor-joining method
• BPROM
• Promoter region

Abstract:

A bacterial strain, designated Aeromonas sp. kumar, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were studied using BPROM tool. In genetics, a promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters are typically located near the genes they regulate, on the same strand and upstream (towards the 5’ region of the sense strand). The objective of the study is to predict the regulatory elements which are -10 box, -35box and three Transcription Factors (rpoD19, rpoD17 and araC) with their binding sites in the 16S rRNA gene of Aeromonas sp. kumar. The gene bank accession number for 16S rRNA gene of Aeromonas sp. kumar is FJ896014.

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Kumar, P., Ramakritinan, C. M., and Kumaraguru, A. K.. 16S rRNA based identification of Aeromonas sp. kumar by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3898.1> (2009)

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