Acquisition of genome information from single-celled unculturable organisms (radiolaria) by exploiting genome profiling (GP)

Mariko Kouduka,Atsushi Matsuoka,Koichi Nishigaki

doi:10.1186/1471-2164-7-135

Mariko Kouduka, Atsushi Matsuoka + Show 1 more

Open Access

https://doi.org/10.1186/1471-2164-7-135

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Journal: BMC Genomics	Publication Date: Jun 2, 2006
Citations: 32	License type: CC BY 2.0

Affiliation: Saitama University, Niigata University

Abstract

BackgroundThere is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather limited amount of genome information. In this paper, we have developed a method which provides a sufficient amount of data from an unculturable organism. The effectiveness of this method was demonstrated by applying it to the provisional classification of a set of unculturable organisms (radiolarians).ResultsDendrogram was drawn regarding the single-celled unculturable species based on the similarity score termed PaSS, offering a consistent result with the conventional taxonomy of them built up based on phenotypes. This fact has shown that genome profiling-based technology developed here can obtain genome information being sufficient for identifying and classifying species from a single-celled organism.ConclusionSince this method is so simple, general, and yet powerful, it can be applied to various organisms and cells, especially single-celled, uncluturable ones, for their genome analysis.

Highlights

There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians
This is by no means an easy task because of the difficulty in collecting samples, and the additional complication that each organism is composed of only a single cell, and methods for culturing Radiolaria in the laboratory are not available
In this paper we developed a potent method to obtain genome information from unculturable and single-celled organisms

Summary

Introduction

There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians Even worse, such organisms are often very difficult to collect. The gene encoding a small subunit of ribosomal RNA (18S rDNA) has been used for classifying species of Radiolaria, which are taxonomically controversial [3,4,5] This is by no means an easy task because of the difficulty in collecting samples, and the additional complication that each organism is composed of only a single cell, and methods for culturing Radiolaria in the laboratory are not available.

Methods

Results

Conclusion