Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Isolation and Culture Conditions
2.2. Total DNA Extraction
2.3. ONT Library Preparation and Genome Sequencing
2.4. De Novo Hybrid Assembly
2.5. Structural and Functional Annotation
2.6. AT-Rich Regions
2.7. Comparative Genomics
2.8. Pathogenicity- and Virulence-Related Genes
3. Results
3.1. Genome Sequencing and De Novo Assembly
3.2. Structural and Functional Annotation
3.3. Repetitive Elements and AT-Rich Regions
3.4. Secondary Metabolites and Carbohydrate-Active Enzymes
3.5. Orthogroups Inference
3.6. Entomopathogenic Fungus-Related Features
3.7. Evaluation of the Secretome Features with Virulence Function
4. Discussion and 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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Summary Statistics | A. muscarius AC3 |
---|---|
Assembly Statistics | |
# contigs | 39 |
Largest contig | 7,812,308 |
Total length | 36,760,018 |
N50 | 3,276,623 |
L50 | 3 |
GC (%) | 53.44 |
Mismatches | |
# N’s per 100 kbp | 0 |
# N’s | 0 |
BUSCO completeness | |
BUSCO completeness | 99.5% |
Complete | 4472 |
Single-copy | 4460 |
Duplicated | 12 |
Fragmented | 3 |
Missing | 19 |
Protein coding genes | |
Protein coding genes | 10,901 |
Predicted tRNAs | 133 |
Proteins with signal peptide | 1077 |
Predicted effector proteins | 300 |
Predicted cytoplasmic effectors | 88 |
Predicted apoplastic effectors | 212 |
Orthogroup | Gene_Name | Function | Accession Number |
---|---|---|---|
OG0004073 | Bbac | cAMP signaling | EJP69082.1 |
OG0005551 | Bbagt1 | α-glucose transporter | AFN69126.1 |
OG0000595, OG0000996, OG0001347, OG0001550, OG0003256, OG0004772, OG0004773, OG0006500, OG0007415 | Bbbeas | Beauvericina toxin | ACI30659.1, ACI30658.1, ACI30657.1 ACI30656.1, ACI30655.1.ACI30654.1 ACI30653.1.ACI30652.1, ACI30651.1 |
OG0005080 | Bbbsls | Bassianolide synthetase | ACR78148.1, ACR78134.1 |
OG0006326 | Bbchit1 | chitinase | AAN41259.1 |
OG0002032 | BbCreA | CreA Aspergillus | AXG50936.1 |
OG0002053 | Bbcsa1 | Neuronal calcium sensor | AFG25510.1 |
OG0000010 | Bbcyp52x1 | Predicted_cytochrome_P450 | ADK36660.1 |
OG0001161 | Bbgas1 | Cell-wall anchored enzyme | ADP22300.1 |
OG0000852 | BbGPCR3 | G-protein coupled receptor | XP_008594187.1 |
OG0001208 | Bbhog1 | MAP kinase | AAS77871.1 |
OG0002187 | Bbjen1 | Carboxylate transporter | AAO33825.1 |
OG0003168 | Bbmpd | Mannitol-1-phosphate-dehydrogenase | ACU32784.1 |
OG0003410 | Bbmpk1 | MAP kinase | AAQ24633.1 |
OG0001461 | Bbmsn2 | Transcription factor | EJP70102.1 |
OG0001442 | Bbmtd | Mannitol dehydrogenase | ADV16370.1 |
OG0000103 | BbmtrA | Putative methyltransferase | EJP69472.1 |
OG0000771 | Bbpmr1 | ATPase, signaling | AAY40175 |
OG0005594 | Bbrgs1 | G-protein signaling | ABL61517.1 |
OG0000669 | Bbslt2 | MAP kinase | AEU60018.1 |
OG0005917 | Bbsnf1 | Protein kinase | XP_008597580.1 |
OG0003206, OG0009475, OG0000753, OG0000172 | cat-A, cat-B, cat-C, cat-D | Catalase A, B C and catalase D | JX050138.1, JX050139.1.JX050141.1, JX050142, JX050140 |
OG0005553 | cdc14 | Dual specificity phosphatase | EJP63157.1 |
OG0004028 | cdc25 | Regulates Cdk1 activity | EJP68939 |
OG0000004 | cdep1 | Cuticle-degrading_proteinase_CDEP-1 | AAK70804.1 |
OG0000261 | CnA1, CnA2, CnB, Crz1 | Calcineuring-mediated phosphatase | XP_008596022.1 |
OG0000461 | Fkh2 | Transcription factor | EJP62625.1 |
OG0007102, OG0006455 | Hyd1, hyd2 | Hydrophobin, hydrophobin | ABO38181 |
ABP58683.1 | |||
OG0002106, OG0002128, OG0002169 | ktr1, ktr2, ktr4 | a-1,2-mannosyltransferase | EJP63998.1, EJP62226.1, EJP69973.1 |
OG0001805 | Mdr1 | ABC transporters | XP_008595100, XP_008602098.1, XP_008600979.1, XP_008594344.1, |
OG0000167 | Pdr1, Pdr2 | ABC transporters | XP_008595100, XP_008602098.1, XP_008600979.1, XP_008594344.1, |
OG0001832 | Pdr5 | ABC transporters | XP_008595100, XP_008602098.1, XP_008600979.1, XP_008594344.1, |
OG0006835 | ras1, ras2, ras3 | GTPase, signal transduction | EJP70406.1 |
OG0005188 | sod1-5 | Superoxide dismutases | EJP67024.1 |
OG0006040 | trx1-6 | Thioredoxin antioxidants | ACT21200.1 |
OG0002437, OG0003500, OG0004231, OG0004459, OG0008389 | vcx1A-E | Calcium/proton exchanger | EJP69434.1, EJP63266.1, EJP67299.1, EJP69455.1, EJP69457.1 |
OG0001590 | wee1 | Regulates Cdk1 activity | EJP62459 |
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Turco, S.; Drais, M.I.; Rossini, L.; Di Sora, N.; Brugneti, F.; Speranza, S.; Contarini, M.; Mazzaglia, A. Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds. Genes 2024, 15, 993. https://doi.org/10.3390/genes15080993
Turco S, Drais MI, Rossini L, Di Sora N, Brugneti F, Speranza S, Contarini M, Mazzaglia A. Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds. Genes. 2024; 15(8):993. https://doi.org/10.3390/genes15080993
Chicago/Turabian StyleTurco, Silvia, Mounira Inas Drais, Luca Rossini, Nicolò Di Sora, Federico Brugneti, Stefano Speranza, Mario Contarini, and Angelo Mazzaglia. 2024. "Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds" Genes 15, no. 8: 993. https://doi.org/10.3390/genes15080993