Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).

DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial...

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Autores principales:	Ian A Luddington, Irena Kaczmarska, Connie Lovejoy
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fcd3677d634a4e65bca0748d067b7faa
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spelling	oai:doaj.org-article:fcd3677d634a4e65bca0748d067b7faa2021-11-18T07:04:33ZDistance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).1932-620310.1371/journal.pone.0045664https://doaj.org/article/fcd3677d634a4e65bca0748d067b7faa2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029169/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.Ian A LuddingtonIrena KaczmarskaConnie LovejoyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45664 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ian A Luddington Irena Kaczmarska Connie Lovejoy Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
description	DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.
format	article
author	Ian A Luddington Irena Kaczmarska Connie Lovejoy
author_facet	Ian A Luddington Irena Kaczmarska Connie Lovejoy
author_sort	Ian A Luddington
title	Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
title_short	Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
title_full	Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
title_fullStr	Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
title_full_unstemmed	Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).
title_sort	distance and character-based evaluation of the v4 region of the 18s rrna gene for the identification of diatoms (bacillariophyceae).
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/fcd3677d634a4e65bca0748d067b7faa
work_keys_str_mv	AT ianaluddington distanceandcharacterbasedevaluationofthev4regionofthe18srrnagenefortheidentificationofdiatomsbacillariophyceae AT irenakaczmarska distanceandcharacterbasedevaluationofthev4regionofthe18srrnagenefortheidentificationofdiatomsbacillariophyceae AT connielovejoy distanceandcharacterbasedevaluationofthev4regionofthe18srrnagenefortheidentificationofdiatomsbacillariophyceae
_version_	1718424017139924992

Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).

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