Extensive intragenomic variation in the internal transcribed spacer region of fungi
Summary: Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studi...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-08-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223013949 |
| _version_ | 1827897252988846080 |
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| author | Michael J. Bradshaw M. Catherine Aime Antonis Rokas Autumn Maust Swarnalatha Moparthi Keila Jellings Alexander M. Pane Dylan Hendricks Binod Pandey Yuanning Li Donald H. Pfister |
| author_facet | Michael J. Bradshaw M. Catherine Aime Antonis Rokas Autumn Maust Swarnalatha Moparthi Keila Jellings Alexander M. Pane Dylan Hendricks Binod Pandey Yuanning Li Donald H. Pfister |
| author_sort | Michael J. Bradshaw |
| collection | DOAJ |
| description | Summary: Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi. |
| first_indexed | 2024-03-12T22:46:32Z |
| format | Article |
| id | doaj.art-cbec43bdf1c84624a3107d05bd8cd77b |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-12T22:46:32Z |
| publishDate | 2023-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-cbec43bdf1c84624a3107d05bd8cd77b2023-07-21T05:00:06ZengElsevieriScience2589-00422023-08-01268107317Extensive intragenomic variation in the internal transcribed spacer region of fungiMichael J. Bradshaw0M. Catherine Aime1Antonis Rokas2Autumn Maust3Swarnalatha Moparthi4Keila Jellings5Alexander M. Pane6Dylan Hendricks7Binod Pandey8Yuanning Li9Donald H. Pfister10Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Corresponding authorDepartment of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USADepartment of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USASchool of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USADepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USADepartment of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USASchool of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USASchool of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USADepartment of Plant Pathology, North Dakota State University, Fargo, ND 58102, USAInstitute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, ChinaHarvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USASummary: Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.http://www.sciencedirect.com/science/article/pii/S2589004223013949Molecular biologyMicrobiologyEvolutionary biology |
| spellingShingle | Michael J. Bradshaw M. Catherine Aime Antonis Rokas Autumn Maust Swarnalatha Moparthi Keila Jellings Alexander M. Pane Dylan Hendricks Binod Pandey Yuanning Li Donald H. Pfister Extensive intragenomic variation in the internal transcribed spacer region of fungi iScience Molecular biology Microbiology Evolutionary biology |
| title | Extensive intragenomic variation in the internal transcribed spacer region of fungi |
| title_full | Extensive intragenomic variation in the internal transcribed spacer region of fungi |
| title_fullStr | Extensive intragenomic variation in the internal transcribed spacer region of fungi |
| title_full_unstemmed | Extensive intragenomic variation in the internal transcribed spacer region of fungi |
| title_short | Extensive intragenomic variation in the internal transcribed spacer region of fungi |
| title_sort | extensive intragenomic variation in the internal transcribed spacer region of fungi |
| topic | Molecular biology Microbiology Evolutionary biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223013949 |
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