Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland
The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights t...
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ftpubmed:oai:pubmedcentral.nih.gov:10210050 2023-06-11T04:13:05+02:00 Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland Xu, Maonian Liu, Yingkui Möller, Erik LaGreca, Scott Moya, Patricia Wang, Xinyu Timdal, Einar de Boer, Hugo Barreno, Eva Wang, Lisong Thüs, Holger Andrésson, Ólafur Magnússon, Kristinn Pétur Ólafsdóttir, Elín Soffia Heiðmarsson, Starri 2023-03-21 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210050/ https://doi.org/10.3897/mycokeys.96.100037 en eng Pensoft Publishers http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210050/ http://dx.doi.org/10.3897/mycokeys.96.100037 Maonian Xu, Yingkui Liu, Erik Möller, Scott LaGreca, Patricia Moya, Xinyu Wang, Einar Timdal, Hugo de Boer, Eva Barreno, Lisong Wang, Holger Thüs, Ólafur Andrésson, Kristinn Pétur Magnússon, Elín Soffia Ólafsdóttir, Starri Heiðmarsson https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. MycoKeys Research Article Text 2023 ftpubmed https://doi.org/10.3897/mycokeys.96.100037 2023-05-28T01:08:57Z The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophoracarrionii and Lichenotheliaconvexa. New mycobiont-specific primers (mt-SSU-581-5’ and mt-SSU-1345-3’) were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics. Text Iceland PubMed Central (PMC) MycoKeys 96 57 75 |
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Research Article Xu, Maonian Liu, Yingkui Möller, Erik LaGreca, Scott Moya, Patricia Wang, Xinyu Timdal, Einar de Boer, Hugo Barreno, Eva Wang, Lisong Thüs, Holger Andrésson, Ólafur Magnússon, Kristinn Pétur Ólafsdóttir, Elín Soffia Heiðmarsson, Starri Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
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Research Article |
description |
The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophoracarrionii and Lichenotheliaconvexa. New mycobiont-specific primers (mt-SSU-581-5’ and mt-SSU-1345-3’) were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics. |
format |
Text |
author |
Xu, Maonian Liu, Yingkui Möller, Erik LaGreca, Scott Moya, Patricia Wang, Xinyu Timdal, Einar de Boer, Hugo Barreno, Eva Wang, Lisong Thüs, Holger Andrésson, Ólafur Magnússon, Kristinn Pétur Ólafsdóttir, Elín Soffia Heiðmarsson, Starri |
author_facet |
Xu, Maonian Liu, Yingkui Möller, Erik LaGreca, Scott Moya, Patricia Wang, Xinyu Timdal, Einar de Boer, Hugo Barreno, Eva Wang, Lisong Thüs, Holger Andrésson, Ólafur Magnússon, Kristinn Pétur Ólafsdóttir, Elín Soffia Heiðmarsson, Starri |
author_sort |
Xu, Maonian |
title |
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
title_short |
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
title_full |
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
title_fullStr |
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
title_full_unstemmed |
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland |
title_sort |
mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal dna: a focus on the lichenized fungal genus melanelia (ascomycota, parmeliaceae) in iceland |
publisher |
Pensoft Publishers |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210050/ https://doi.org/10.3897/mycokeys.96.100037 |
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Iceland |
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Iceland |
op_source |
MycoKeys |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210050/ http://dx.doi.org/10.3897/mycokeys.96.100037 |
op_rights |
Maonian Xu, Yingkui Liu, Erik Möller, Scott LaGreca, Patricia Moya, Xinyu Wang, Einar Timdal, Hugo de Boer, Eva Barreno, Lisong Wang, Holger Thüs, Ólafur Andrésson, Kristinn Pétur Magnússon, Elín Soffia Ólafsdóttir, Starri Heiðmarsson https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_doi |
https://doi.org/10.3897/mycokeys.96.100037 |
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96 |
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57 |
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75 |
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1768389689138479104 |