Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Overview of Our Analysis Idea
2.2. Data Download
2.3. Orthologous Groups and Separation
2.4. Transmembrane Domain (TM) Prediction
2.5. Horizontal Gene Transfer (HGT) Prediction
2.6. Annotation Enrichment
2.7. Phylogram and Heatmap Figure Construction
2.8. Data and Code Availability
3. Results
3.1. Orthogroup Categorization Shows That ~20% Orthogroups Are Group-Specific and Accessory
3.2. Species Phylogeny Reveals That Phytopathogenicity Is Not Phylogenetically Determined
3.3. Group-Specific Orthogroups Have More Enriched Functional Terms than Accessory Orthogroups
3.4. Secreted Proteins with Signal Peptides Show Higher Significance in Group-Specific Orthogroups than in Accessory Orthogroups
3.5. HGTs Show Higher Significance and Higher Occurrence in Group-Specific Orthogroups than in Accessory Orthogroups
3.6. Phytopathogenic Fungi Have More Enriched Functional Terms in Group-Specific Orthogroups than Accessory Orthogroups
3.7. More Phytopathogenic Fungi than Non-Phytopathogenic Fungi Are Found to Have a Larger Number of Enriched Functional Terms in Group-Specific Orthogroups
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Enriched Terms | Description | # of Species (% of Total 92) | # of P Species (% of Total 68) | # of NP Species (% of Total 24) |
---|---|---|---|---|
Signal Pep | Signal peptide | 79 (85.9%) | 60 (88.2%) * | 19 (79.2%) |
HGT | horizontal gene transfer | 55 (59.8%) | 38 (55.9%) | 17 (70.8%) |
KOG1216 | Von Willebrand factor and related coagulation proteins | 20 (21.7%) | 16 (23.5%) * | 4 (16.7%) |
KOG3599 | Ca2+-modulated nonselective cation channel polycystin | 17 (18.5%) | 16 (23.5%) * | 1 (4.2%) |
KOG4157 | beta-1,6-N-acetylglucosaminyltransferase, contains WSC domain | 13 (14.1%) | 9 (13.2%) | 4 (16.7%) |
KOG2992 | Nucleolar GTPase/ATPase p130 | 10 (10.9%) | 7 (10.3%) | 3 (12.5%) |
IPR001810 | Cyclin-like F-box | 9 (9.8%) | 3 (4.4%) | 6 (25.0%) |
IPR003014 | N/apple PAN | 9 (9.8%) | 9 (13.2%) * | 0 |
KOG0161 | Myosin class II heavy chain | 9 (9.8%) | 7 (10.3%) * | 2 (8.3%) |
IPR003609 | Apple-like | 8 (8.7%) | 8 (11.8%) * | 0 |
KOG4297 | C-type lectin | 8 (8.7%) | 7 (10.3%) * | 1 (4.2%) |
JGI ID * | Species | Species Type | Taxonomy Class | # of Enriched Terms |
---|---|---|---|---|
Zymps1 | Zymoseptoria pseudotritici | P | Dothideomycetes | 21 |
Mycgr3 | Mycosphaerella graminicola | P | Dothideomycetes | 16 |
Chove1 | Choiromyces venosus | NP | Pezizomycetes | 14 |
Tubma1 | Tuber magnatum | NP | Pezizomycetes | 10 |
Zymar1 | Zymoseptoria ardabiliae | P | Dothideomycetes | 10 |
Clafu1 | Cladosporium fulvum | P | Dothideomycetes | 9 |
Erynec1 | Erysiphe necator | P | Leotiomycetes | 9 |
Fusgr1 | Fusarium graminearum | P | Sordariomycetes | 8 |
Fusve2 | Fusarium verticillioides | P | Sordariomycetes | 8 |
Venin1 | Venturia inaequalis | P | Dothideomycetes | 8 |
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Peterson, D.; Li, T.; Calvo, A.M.; Yin, Y. Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. J. Fungi 2021, 7, 337. https://doi.org/10.3390/jof7050337
Peterson D, Li T, Calvo AM, Yin Y. Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. Journal of Fungi. 2021; 7(5):337. https://doi.org/10.3390/jof7050337
Chicago/Turabian StylePeterson, Daniel, Tang Li, Ana M. Calvo, and Yanbin Yin. 2021. "Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity" Journal of Fungi 7, no. 5: 337. https://doi.org/10.3390/jof7050337
APA StylePeterson, D., Li, T., Calvo, A. M., & Yin, Y. (2021). Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. Journal of Fungi, 7(5), 337. https://doi.org/10.3390/jof7050337