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Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)

Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search...

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Autores principales: Krawczyk, Katarzyna, Nobis, Marcin, Myszczyński, Kamil, Klichowska, Ewelina, Sawicki, Jakub
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792575/
https://www.ncbi.nlm.nih.gov/pubmed/29386579
http://dx.doi.org/10.1038/s41598-018-20399-w
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author Krawczyk, Katarzyna
Nobis, Marcin
Myszczyński, Kamil
Klichowska, Ewelina
Sawicki, Jakub
author_facet Krawczyk, Katarzyna
Nobis, Marcin
Myszczyński, Kamil
Klichowska, Ewelina
Sawicki, Jakub
author_sort Krawczyk, Katarzyna
collection PubMed
description Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn’t reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn’t allow for discrimination of all the analyzed taxa of feather grasses.
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spelling pubmed-57925752018-02-12 Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa) Krawczyk, Katarzyna Nobis, Marcin Myszczyński, Kamil Klichowska, Ewelina Sawicki, Jakub Sci Rep Article Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn’t reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn’t allow for discrimination of all the analyzed taxa of feather grasses. Nature Publishing Group UK 2018-01-31 /pmc/articles/PMC5792575/ /pubmed/29386579 http://dx.doi.org/10.1038/s41598-018-20399-w Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Krawczyk, Katarzyna
Nobis, Marcin
Myszczyński, Kamil
Klichowska, Ewelina
Sawicki, Jakub
Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title_full Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title_fullStr Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title_full_unstemmed Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title_short Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
title_sort plastid super-barcodes as a tool for species discrimination in feather grasses (poaceae: stipa)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792575/
https://www.ncbi.nlm.nih.gov/pubmed/29386579
http://dx.doi.org/10.1038/s41598-018-20399-w
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