DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico

Abstract DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these for...

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Autores principales:	Sonia Trujillo-Argueta, Rafael F. del Castillo, Daniel Tejero-Diez, Carlos Alberto Matias-Cervantes, Abril Velasco-Murguía
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3a1320300ab14a269bc2c6d2c2289b7c
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spelling	oai:doaj.org-article:3a1320300ab14a269bc2c6d2c2289b7c2021-11-28T12:16:24ZDNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico10.1038/s41598-021-02237-82045-2322https://doaj.org/article/3a1320300ab14a269bc2c6d2c2289b7c2021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-02237-8https://doaj.org/toc/2045-2322Abstract DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.Sonia Trujillo-ArguetaRafael F. del CastilloDaniel Tejero-DiezCarlos Alberto Matias-CervantesAbril Velasco-MurguíaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sonia Trujillo-Argueta Rafael F. del Castillo Daniel Tejero-Diez Carlos Alberto Matias-Cervantes Abril Velasco-Murguía DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
description	Abstract DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.
format	article
author	Sonia Trujillo-Argueta Rafael F. del Castillo Daniel Tejero-Diez Carlos Alberto Matias-Cervantes Abril Velasco-Murguía
author_facet	Sonia Trujillo-Argueta Rafael F. del Castillo Daniel Tejero-Diez Carlos Alberto Matias-Cervantes Abril Velasco-Murguía
author_sort	Sonia Trujillo-Argueta
title	DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
title_short	DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
title_full	DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
title_fullStr	DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
title_full_unstemmed	DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico
title_sort	dna barcoding ferns in an unexplored tropical montane cloud forest area of southeast oaxaca, mexico
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3a1320300ab14a269bc2c6d2c2289b7c
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DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico

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