Taming the beast : a revised classification of Cortinariaceae based on genomic data
Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius...
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/354012 2024-01-07T09:41:58+01:00 Taming the beast : a revised classification of Cortinariaceae based on genomic data Liimatainen, Kare Kim, Jan T. Pokorny, Lisa Kirk, Paul M. Dentinger, Bryn Niskanen, Tuula University of Helsinki Finnish Museum of Natural History 2023-02-01T13:20:01Z 82 application/pdf http://hdl.handle.net/10138/354012 eng eng Springer 10.1007/s13225-022-00499-9 Liimatainen , K , Kim , J T , Pokorny , L , Kirk , P M , Dentinger , B & Niskanen , T 2022 , ' Taming the beast : a revised classification of Cortinariaceae based on genomic data ' , Fungal diversity : an international journal of mycology , vol. 112 , no. 1 , pp. 89-170 . https://doi.org/10.1007/s13225-022-00499-9 c76244ac-e321-4a3e-a53f-a4e57d69b5bf http://hdl.handle.net/10138/354012 000760152400001 cc_by openAccess info:eu-repo/semantics/openAccess Agaricales Fungariomics Fungi HybPiper Museomics Targeted capture sequencing Whole genome sequencing 11831 Plant biology Article publishedVersion 2023 ftunivhelsihelda 2023-12-14T00:09:53Z Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera-Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius-is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and ... Article in Journal/Newspaper Arctic HELDA – University of Helsinki Open Repository Arctic Fungal Diversity 112 1 89 170 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
Agaricales Fungariomics Fungi HybPiper Museomics Targeted capture sequencing Whole genome sequencing 11831 Plant biology |
spellingShingle |
Agaricales Fungariomics Fungi HybPiper Museomics Targeted capture sequencing Whole genome sequencing 11831 Plant biology Liimatainen, Kare Kim, Jan T. Pokorny, Lisa Kirk, Paul M. Dentinger, Bryn Niskanen, Tuula Taming the beast : a revised classification of Cortinariaceae based on genomic data |
topic_facet |
Agaricales Fungariomics Fungi HybPiper Museomics Targeted capture sequencing Whole genome sequencing 11831 Plant biology |
description |
Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera-Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius-is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and ... |
author2 |
University of Helsinki Finnish Museum of Natural History |
format |
Article in Journal/Newspaper |
author |
Liimatainen, Kare Kim, Jan T. Pokorny, Lisa Kirk, Paul M. Dentinger, Bryn Niskanen, Tuula |
author_facet |
Liimatainen, Kare Kim, Jan T. Pokorny, Lisa Kirk, Paul M. Dentinger, Bryn Niskanen, Tuula |
author_sort |
Liimatainen, Kare |
title |
Taming the beast : a revised classification of Cortinariaceae based on genomic data |
title_short |
Taming the beast : a revised classification of Cortinariaceae based on genomic data |
title_full |
Taming the beast : a revised classification of Cortinariaceae based on genomic data |
title_fullStr |
Taming the beast : a revised classification of Cortinariaceae based on genomic data |
title_full_unstemmed |
Taming the beast : a revised classification of Cortinariaceae based on genomic data |
title_sort |
taming the beast : a revised classification of cortinariaceae based on genomic data |
publisher |
Springer |
publishDate |
2023 |
url |
http://hdl.handle.net/10138/354012 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
10.1007/s13225-022-00499-9 Liimatainen , K , Kim , J T , Pokorny , L , Kirk , P M , Dentinger , B & Niskanen , T 2022 , ' Taming the beast : a revised classification of Cortinariaceae based on genomic data ' , Fungal diversity : an international journal of mycology , vol. 112 , no. 1 , pp. 89-170 . https://doi.org/10.1007/s13225-022-00499-9 c76244ac-e321-4a3e-a53f-a4e57d69b5bf http://hdl.handle.net/10138/354012 000760152400001 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
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Fungal Diversity |
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112 |
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1 |
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89 |
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170 |
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