Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron Article Swipe
Marjorie Cedeño‐Sanchez
,
Tian Cheng
,
Christopher Lambert
,
Miroslav Kolařík
,
Eric Kuhnert
,
Russell J. Cox
,
Jörn Kalinowski
,
Bart Verwaaijen
,
Marc Stadler
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1007/s11557-023-01940-2
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1007/s11557-023-01940-2
Sequencing ribosomal DNA loci, such as ITS and LSU, are among the first steps to characterize and identify newly isolated fungal strains. Substantial doubt has recently been raised concerning the unequivocal suitability of using this sequence information for inferring inter- and intraspecific relationships, as especially the ITS locus was repeatedly shown to harbor high intragenomic plasticity. The evolutionary mechanisms leading to this phenomenon are poorly understood, but this is about to change, owing to the availability of third generation sequencing techniques. The current study attempts a comprehensive analysis of rDNA cistrons in the genomes of over 40 selected species of Hypoxylaceae ( Xylariales ), using a combination of 2nd generation (Illumina) and 3rd generation sequencing technologies (Oxford Nanopore), along with extensive usage of bioinformatic tools to obtain high-quality genomes. Our findings revealed high intragenomic polymorphisms in distinct Hypoxylaceae species, indicating the presence of deep rDNA paralogs. Phylogenetic inference of the ITS rDNA showed low support for the primary clades within Hypoxylaceae , while inference using the protein encoding gene RPB2 showed better support. We also found that proteinogenic genes are not prone to intraspecific and intragenomic polymorphisms as much as the rDNA loci. Our study highlights the limitations of solely relying on the rDNA cistron as a barcode for fungi. We propose TUB2 as a new primary barcoding marker for Hypoxylaceae and other Xylariales . Moreover, we demonstrate the feasibility to retrieve some DNA loci that had hitherto not been used for classical phylogenetic studies (such as TEF1 ) in Xylariales directly from genomes without the necessity to work with primers.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1007/s11557-023-01940-2
- https://link.springer.com/content/pdf/10.1007/s11557-023-01940-2.pdf
- OA Status
- hybrid
- Cited By
- 12
- References
- 46
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4390392661
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Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4390392661Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1007/s11557-023-01940-2Digital Object Identifier
- Title
-
Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistronWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
-
2023-12-29Full publication date if available
- Authors
-
Marjorie Cedeño‐Sanchez, Tian Cheng, Christopher Lambert, Miroslav Kolařík, Eric Kuhnert, Russell J. Cox, Jörn Kalinowski, Bart Verwaaijen, Marc StadlerList of authors in order
- Landing page
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https://doi.org/10.1007/s11557-023-01940-2Publisher landing page
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https://link.springer.com/content/pdf/10.1007/s11557-023-01940-2.pdfDirect link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
- OA URL
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https://link.springer.com/content/pdf/10.1007/s11557-023-01940-2.pdfDirect OA link when available
- Concepts
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Biology, Genome, Cistron, Phylogenetic tree, Genetics, Evolutionary biology, DNA sequencing, Phylogenetics, Gene, Escherichia coliTop concepts (fields/topics) attached by OpenAlex
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12Total citation count in OpenAlex
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2025: 7, 2024: 5Per-year citation counts (last 5 years)
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46Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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