Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Yeast Assemblies Used in This Study
2.2. Species Delineation Using ANI Calculation, In Silico Alignment of D1/D2 Region of LSU Ribosomal DNA, and the Selection of Orthologous Genes (MAOG)
2.3. Statistical Analysis for the Comparison between D1/D2 Sequence, MAOG, and ANI Calculation
3. Results
3.1. Species Delineation Based on ANI Calculation
3.2. Species Delineation Based on In Silico Extraction of D1/D2 Region and MAOG
3.3. Comparative Analysis between D1/D2 Sequence Alignments, MAOG, and ANI
3.4. Exploring Species Delineation in Saccharomyces Hybrid Genomes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genus | Within-Species Cutoff | Between-Species Cutoff |
---|---|---|
Candida | >96% | <88% |
Debaryomyces | >92% | <90% |
Hanseniaspora | >97% | <90% |
Kazachstania | >98% | <89% |
Kluyveromyces | >95% | <79% |
Pichia | >98% | <82% |
Rhodotorula | >95% | <80% |
Saccharomyces | >92% | <81% |
Schizosaccharomyces | >98% | <80% |
Starmerella | >97% | <85% |
Torulaspora | >95% | <90% |
Yarrowia | >98% | <90% |
Genus | Total N° of Assemblies | N° of Assemblies Analyzed by FastANI | N° of Assemblies Analyzed by MAOG | N° of Assemblies Analyzed by D1/D2 Alignment | N° of Assemblies Analyzed by All Three Methods |
---|---|---|---|---|---|
Pichia | 32 | 32 | 32 | 23 | 23 |
Kazachstania | 28 | 28 | 20 | 17 | 16 |
Candida | 114 | 114 | 104 | 34 | 29 |
Saccharomyces | 148 | 148 | 121 | 86 | 80 |
Debaryomyces | 19 | 19 | 15 | 10 | 8 |
Rhodotorula | 132 | 132 | 47 | 115 | 36 |
Starmerella | 20 | 20 | 20 | 14 | 14 |
Yarrowia | 39 | 39 | 28 | 15 | 9 |
Schizosaccharomyces | 23 | 23 | 23 | 20 | 20 |
Hanseniaspora | 31 | 31 | 31 | 23 | 23 |
Kluyveromyces | 27 | 27 | 20 | 20 | 14 |
Torulaspora | 31 | 31 | 23 | 27 | 18 |
Total | 644 | 644 | 484 | 404 | 290 |
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Cortimiglia, C.; Alonso-Del-Real, J.; Belloso Daza, M.V.; Querol, A.; Iacono, G.; Cocconcelli, P.S. Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species. J. Fungi 2024, 10, 646. https://doi.org/10.3390/jof10090646
Cortimiglia C, Alonso-Del-Real J, Belloso Daza MV, Querol A, Iacono G, Cocconcelli PS. Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species. Journal of Fungi. 2024; 10(9):646. https://doi.org/10.3390/jof10090646
Chicago/Turabian StyleCortimiglia, Claudia, Javier Alonso-Del-Real, Mireya Viviana Belloso Daza, Amparo Querol, Giovanni Iacono, and Pier Sandro Cocconcelli. 2024. "Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species" Journal of Fungi 10, no. 9: 646. https://doi.org/10.3390/jof10090646