Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)

Abstract Background Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal tra...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Allison L. Graper, Andrzej K. Noyszewski, Neil O. Anderson, Alan G. Smith
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Herbarium specimens DNA barcoding PCR amplification Diagnostic SNPs Botany QK1-989
Acceso en línea:	https://doaj.org/article/7fd9459e38404b8db13ee175fcf56ff3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:7fd9459e38404b8db13ee175fcf56ff3
record_format	dspace
spelling	oai:doaj.org-article:7fd9459e38404b8db13ee175fcf56ff32021-11-07T12:09:43ZVariability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)10.1186/s12870-021-03284-z1471-2229https://doaj.org/article/7fd9459e38404b8db13ee175fcf56ff32021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03284-zhttps://doaj.org/toc/1471-2229Abstract Background Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882–2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species. Results We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin. Conclusions While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.Allison L. GraperAndrzej K. NoyszewskiNeil O. AndersonAlan G. SmithBMCarticleHerbarium specimensDNA barcodingPCR amplificationDiagnostic SNPsBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Herbarium specimens DNA barcoding PCR amplification Diagnostic SNPs Botany QK1-989
spellingShingle	Herbarium specimens DNA barcoding PCR amplification Diagnostic SNPs Botany QK1-989 Allison L. Graper Andrzej K. Noyszewski Neil O. Anderson Alan G. Smith Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
description	Abstract Background Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882–2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species. Results We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin. Conclusions While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.
format	article
author	Allison L. Graper Andrzej K. Noyszewski Neil O. Anderson Alan G. Smith
author_facet	Allison L. Graper Andrzej K. Noyszewski Neil O. Anderson Alan G. Smith
author_sort	Allison L. Graper
title	Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
title_short	Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
title_full	Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
title_fullStr	Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
title_full_unstemmed	Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
title_sort	variability in its1 and its2 sequences of historic herbaria and extant (fresh) phalaris species (poaceae)
publisher	BMC
publishDate	2021
url	https://doaj.org/article/7fd9459e38404b8db13ee175fcf56ff3
work_keys_str_mv	AT allisonlgraper variabilityinits1andits2sequencesofhistoricherbariaandextantfreshphalarisspeciespoaceae AT andrzejknoyszewski variabilityinits1andits2sequencesofhistoricherbariaandextantfreshphalarisspeciespoaceae AT neiloanderson variabilityinits1andits2sequencesofhistoricherbariaandextantfreshphalarisspeciespoaceae AT alangsmith variabilityinits1andits2sequencesofhistoricherbariaandextantfreshphalarisspeciespoaceae
_version_	1718443498178347008

Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)

Ejemplares similares