Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)
Abstract Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and a...
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BMC
2020-12-01
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| Series: | IMA Fungus |
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| Online Access: | https://doi.org/10.1186/s43008-020-00051-x |
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| author | Felix Grewe Claudio Ametrano Todd J. Widhelm Steven Leavitt Isabel Distefano Wetchasart Polyiam David Pizarro Mats Wedin Ana Crespo Pradeep K. Divakar H. Thorsten Lumbsch |
| author_facet | Felix Grewe Claudio Ametrano Todd J. Widhelm Steven Leavitt Isabel Distefano Wetchasart Polyiam David Pizarro Mats Wedin Ana Crespo Pradeep K. Divakar H. Thorsten Lumbsch |
| author_sort | Felix Grewe |
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| description | Abstract Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow. |
| format | Article |
| id | doaj-art-00bd739809424f1fb7f0ead29328a2b9 |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2020-12-01 |
| publisher | BMC |
| record_format | Article |
| series | IMA Fungus |
| spelling | doaj-art-00bd739809424f1fb7f0ead29328a2b92025-02-02T11:23:29ZengBMCIMA Fungus2210-63592020-12-0111111110.1186/s43008-020-00051-xUsing target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)Felix Grewe0Claudio Ametrano1Todd J. Widhelm2Steven Leavitt3Isabel Distefano4Wetchasart Polyiam5David Pizarro6Mats Wedin7Ana Crespo8Pradeep K. Divakar9H. Thorsten Lumbsch10Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular SystematicsScience & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular SystematicsScience & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular SystematicsDepartment of Biology and M. L. Bean Life Science Museum, Brigham Young UniversityScience & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular SystematicsLichen Research Unit, Biology Department, Faculty of Science, Ramkhamhaeng UniversityDepartamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de MadridDepartment of Botany, Swedish Museum of Natural HistoryDepartamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de MadridDepartamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de MadridScience & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular SystematicsAbstract Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.https://doi.org/10.1186/s43008-020-00051-xNext-generation sequencingTarget captureHybPiperPhylogenomicsMaximum likelihoodBayesian interference |
| spellingShingle | Felix Grewe Claudio Ametrano Todd J. Widhelm Steven Leavitt Isabel Distefano Wetchasart Polyiam David Pizarro Mats Wedin Ana Crespo Pradeep K. Divakar H. Thorsten Lumbsch Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) IMA Fungus Next-generation sequencing Target capture HybPiper Phylogenomics Maximum likelihood Bayesian interference |
| title | Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) |
| title_full | Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) |
| title_fullStr | Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) |
| title_full_unstemmed | Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) |
| title_short | Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) |
| title_sort | using target enrichment sequencing to study the higher level phylogeny of the largest lichen forming fungi family parmeliaceae ascomycota |
| topic | Next-generation sequencing Target capture HybPiper Phylogenomics Maximum likelihood Bayesian interference |
| url | https://doi.org/10.1186/s43008-020-00051-x |
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