ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi)
To date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been clai...
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2025-01-01
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| author | Yuveantheni Kalaiventhan Kensuke Seto Matthias Wolf |
| author_facet | Yuveantheni Kalaiventhan Kensuke Seto Matthias Wolf |
| author_sort | Yuveantheni Kalaiventhan |
| collection | DOAJ |
| description | To date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been claimed to not be alignable for this group of organisms. Although the ITS2 is a fast-evolving locus, its secondary structure is well conserved. To improve the accuracy and robustness of Chytridiomycota phylogeny, in this study, we attempt, for the first, time to reconstruct an ITS2 sequence–structure phylogeny using the primary sequence and the secondary structure information simultaneously in inferring alignments and trees. Although currently only possible for a fraction of the available data, we show a well-supported ITS2 tree for selected organisms. The results are promising for further exploration of the large number of available ITS2 sequences. |
| format | Article |
| id | doaj-art-51d814d0d2eb457196032efef1dd2ad9 |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Biology |
| spelling | doaj-art-51d814d0d2eb457196032efef1dd2ad92025-01-24T13:23:23ZengMDPI AGBiology2079-77372025-01-011413610.3390/biology14010036ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi)Yuveantheni Kalaiventhan0Kensuke Seto1Matthias Wolf2Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, GermanyFaculty of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya, Yokohama, Kanagawa 240-8501, JapanDepartment of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, GermanyTo date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been claimed to not be alignable for this group of organisms. Although the ITS2 is a fast-evolving locus, its secondary structure is well conserved. To improve the accuracy and robustness of Chytridiomycota phylogeny, in this study, we attempt, for the first, time to reconstruct an ITS2 sequence–structure phylogeny using the primary sequence and the secondary structure information simultaneously in inferring alignments and trees. Although currently only possible for a fraction of the available data, we show a well-supported ITS2 tree for selected organisms. The results are promising for further exploration of the large number of available ITS2 sequences.https://www.mdpi.com/2079-7737/14/1/36Chytridiomycotainternal transcribed spacer 2ITS2phylogenysecondary structuresequence-structure |
| spellingShingle | Yuveantheni Kalaiventhan Kensuke Seto Matthias Wolf ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) Biology Chytridiomycota internal transcribed spacer 2 ITS2 phylogeny secondary structure sequence-structure |
| title | ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) |
| title_full | ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) |
| title_fullStr | ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) |
| title_full_unstemmed | ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) |
| title_short | ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi) |
| title_sort | its2 rrna gene sequence structure phylogeny of the chytridiomycota opisthokonta fungi |
| topic | Chytridiomycota internal transcribed spacer 2 ITS2 phylogeny secondary structure sequence-structure |
| url | https://www.mdpi.com/2079-7737/14/1/36 |
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