Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.

<h4>Background</h4>Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in a...

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Autores principales:	Shamim Ahmed, Manabu Komori, Sachika Tsuji-Ueno, Miho Suzuki, Akinori Kosaku, Kiyoshi Miyamoto, Koichi Nishigaki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/99ffe2ac4f3d4fb9b61a51b38d329408
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spelling	oai:doaj.org-article:99ffe2ac4f3d4fb9b61a51b38d3294082021-11-18T06:46:52ZGenome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.1932-620310.1371/journal.pone.0023963https://doaj.org/article/99ffe2ac4f3d4fb9b61a51b38d3294082011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21912611/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in ambitious comparative biology studies. However, such technologies are still far from routine-use in species classification studies due to their high costs in terms of labor, equipment and consumables.<h4>Methodology/principal findings</h4>Here, we describe a simple and powerful approach for species classification called genome profiling (GP). The GP method composed of random PCR, temperature gradient gel electrophoresis (TGGE) and computer-aided gel image processing is highly informative and less laborious. For demonstration, we classified 26 species of insects using GP and 18S rDNA-sequencing approaches. The GP method was found to give a better correspondence to the classical phenotype-based approach than did 18S rDNA sequencing employing a congruence value. To our surprise, use of a single probe in GP was sufficient to identify the relationships between the insect species, making this approach more straightforward.<h4>Conclusion/significance</h4>The data gathered here, together with those of previous studies show that GP is a simple and powerful method that can be applied for actually universally identifying and classifying species. The current success supported our previous proposal that GP-based web database can be constructible and effective for the global identification/classification of species.Shamim AhmedManabu KomoriSachika Tsuji-UenoMiho SuzukiAkinori KosakuKiyoshi MiyamotoKoichi NishigakiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e23963 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shamim Ahmed Manabu Komori Sachika Tsuji-Ueno Miho Suzuki Akinori Kosaku Kiyoshi Miyamoto Koichi Nishigaki Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
description	<h4>Background</h4>Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in ambitious comparative biology studies. However, such technologies are still far from routine-use in species classification studies due to their high costs in terms of labor, equipment and consumables.<h4>Methodology/principal findings</h4>Here, we describe a simple and powerful approach for species classification called genome profiling (GP). The GP method composed of random PCR, temperature gradient gel electrophoresis (TGGE) and computer-aided gel image processing is highly informative and less laborious. For demonstration, we classified 26 species of insects using GP and 18S rDNA-sequencing approaches. The GP method was found to give a better correspondence to the classical phenotype-based approach than did 18S rDNA sequencing employing a congruence value. To our surprise, use of a single probe in GP was sufficient to identify the relationships between the insect species, making this approach more straightforward.<h4>Conclusion/significance</h4>The data gathered here, together with those of previous studies show that GP is a simple and powerful method that can be applied for actually universally identifying and classifying species. The current success supported our previous proposal that GP-based web database can be constructible and effective for the global identification/classification of species.
format	article
author	Shamim Ahmed Manabu Komori Sachika Tsuji-Ueno Miho Suzuki Akinori Kosaku Kiyoshi Miyamoto Koichi Nishigaki
author_facet	Shamim Ahmed Manabu Komori Sachika Tsuji-Ueno Miho Suzuki Akinori Kosaku Kiyoshi Miyamoto Koichi Nishigaki
author_sort	Shamim Ahmed
title	Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
title_short	Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
title_full	Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
title_fullStr	Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
title_full_unstemmed	Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.
title_sort	genome profiling (gp) method based classification of insects: congruence with that of classical phenotype-based one.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/99ffe2ac4f3d4fb9b61a51b38d329408
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Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one.

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