Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Material and Culture Conditions
2.2. DNA Extraction
2.3. Genome Sequencing, Assembly, and Prediction
2.4. Dispersed Repeat Sequences and Noncoding tRNA Annotation
2.5. Gene Annotation and Functional Analyses
2.6. Comparative Analyses
3. Results
3.1. Genome Assembly and Genomic Characteristics
3.2. Gene Prediction and Functional Annotation
3.3. Fusicoccin A Biosynthesis
3.4. Virulence Factors, Effectors, and Strategies to Overcome Host Responses
3.5. Cellular Transporters
3.6. Comparative Analyses
3.6.1. Predicted Genes and Genome Statistics
3.6.2. CAZymes
3.6.3. BGCs
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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Genome Features | D. amygdali | D. eres |
---|---|---|
Genome assembled | 51.5 Mbp | 60.8 Mbp |
Number of contigs (>500 bp) | 267 | 2524 |
Largest contig length | 4,327,563 bp | 1,105,552 bp |
N50 contig length | 1,008,325 bp | 169,851 bp |
N75 contig length | 622,097 bp | 74,774 bp |
GC content | 52.1% | 47.6% |
BUSCO * completeness | 98.3% | 98.4% |
Predicted genes | 15,818 | 16,499 |
Predicted proteins with signal peptides | 1874 | 1806 |
Secreted proteins | 1562 | 1616 |
Candidate effectors | 109 | 98 |
Total length of coding genes | 23,649,268 bp | 24,024,391 |
Average length of predicted genes | 1495 bp | 1456 bp |
Total length of predicted genes/Genome assembled | 45.9% | 39.5% |
Average number of exons per gene | 3 | 3 |
Average number of introns per gene | 2 | 2 |
Type a | D. amygdali CAA958 | D. eres CBS 160.32 | |||||
---|---|---|---|---|---|---|---|
Number | Total Length (bp) | Genome Content (%) | Number | Total Length (bp) | Genome Content (%) | ||
Interspersed and terminal repeats | LTRs | 131 | 12,096 | 0.0235 | 140 | 12,642 | 0.0208 |
DNA transposons | 174 | 9942 | 0.0193 | 143 | 11,693 | 0.0192 | |
LINEs | 18 | 1207 | 0.0023 | 21 | 1611 | 0.0027 | |
SINEs | 0 | 0 | 0 | 0 | 0 | 0 | |
Rolling circles | 4 | 243 | 0.0005 | 0 | 0 | 0 | |
Small RNA | 55 | 8582 | 0.0167 | 52 | 8523 | 0.0140 | |
Satellites | 25 | 1927 | 0.0037 | 18 | 1434 | 0.0024 | |
Simple repeats | 11,895 | 486,262 | 0.9445 | 15,264 | 686,233 | 1.1289 | |
Low complexity | 1067 | 51,681 | 0.1004 | 1571 | 77,250 | 0.1271 | |
TOTAL | 13,369 | 571,940 | 1.1109 | 17,209 | 799,386 | 1.3151 | |
Tandem repeats | 8639 | 478,007 | 0.9459 | 33,522 | 2,237,060 | 3.6802 | |
tRNAs | 162 | 15,038 | 0.0292 | 177 | 17,216 | 0.0283 |
Putative Protein | D. amygdali CAA958 | D. eres CBS 160.32 | Function | References |
---|---|---|---|---|
Acid aspartase | √ | × | Role in the mechanisms of virulence during fungal infection, participating in the degradation of the host’s physical barriers | [48] |
Aminobutyrate aminotransferase | √ | √ | Metabolization of γ-aminobutyric acid, providing pathogen nitrogen requirements during infection | [49] |
Aminopeptidase, carboxypeptidase | √ | √ | Protease required by fungi for host peptide degradation during pathogenesis | [50] |
Cerato-ulmi | √ | × | Hydrophobic proteins secreted by filamentous fungi (Ophiostoma species). It possesses properties of a wilt toxin in susceptible elms, such as Ulmus americana | [51,52] |
Chitin synthases | √ | √ | Enzymes that serve as a pathogen-associated molecular pattern (PAMP), triggering immune responses in host plants. Reported in Magnaporthe oryzae, Botrytis cinerea, Fusarium graminearum, and F. verticillioides | [53] |
Metalloprotease | √ | √ | Zinc-chelating protease that plays an essential role in microbial pathogenesis. In M. oryzae, it is an effector that triggers host defense response | [54] |
Nudix proteins | √ | √ | Important virulence components manipulating host defense mechanisms | [55] |
Siderophores | √ | √ | Chelators synthesized to be involved in iron uptake, intracellular transport, and storage. Essential virulence factors allow the fungus to overcome severe iron limitation imposed by the host | [56] |
Subtilisin-like serine protease | √ | √ | Proteases that are released in infected plant host to degrade pathogenesis-related proteins and disrupt host cell membranes | [57] |
Tripeptidyl-peptidase | √ | × | Acidification of the microenvironment in the host facilitates the proliferation of the pathogen | [58] |
Velvet proteins | √ | √ | Promotion of chromatin accessibility and expression of biosynthetic gene clusters involved in pathogenicity as mycotoxins, pigments, and hormones | [59] |
Virulence protein SSD1 | √ | √ | Important for M. grisea to colonize rice leaves, leading to evasion and tolerance of the host immune response | [60,61] |
Vacuole protein sorting | √ | √ | Proteins involved in the delivery of soluble vacuolar compounds, metabolite storage, and osmoregulation. Essential for fungal growth and pathogenesis | [62] |
Transporter Class | D. amygdali CAA958 | D. eres CBS 160.32 |
---|---|---|
Channels and pores (TC 1) | 348 | 348 |
Electrochemical potential-driven transporters (TC 2) | 973 | 911 |
Primary active transporters (TC 3) | 366 | 371 |
Group translocators (TC 4) | 48 | 39 |
Transmembrane electron carriers (TC 5) | 14 | 13 |
Accessory factors involved in transport (TC 8) | 270 | 266 |
Incompletely characterized transport systems (TC 9) | 306 | 290 |
TOTAL | 2325 | 2238 |
Species | Strain | Host | BUSCO * Completeness % | Genome Size (Mb) | GC Content % | Predicted Genes | Secreted Proteins | CAZymes | BGCs | GenBank Accession Number |
---|---|---|---|---|---|---|---|---|---|---|
Diaporthe ampelina | DA912 | Grapevine | 98.7 | 53.4 | 52.8 | 10,704 | ND | 696 | 105 | LWAD01000000 |
Diaporthe amygdali | CAA958 | Blueberry | 98.3 | 51.5 | 52.1 | 15,818 | 1562 | 856 | 86 | This study |
Diaporthe batatas | CRI 302-4 | Sweet potato | 97.9 | 54.4 | 50.6 | 13,037 | 1224 | 941 | 91 | JAHWGW000000000 |
Diaporthe capsici | GY-Z16 | Walnut | 98.4 | 57.6 | 51.3 | 14,425 | 1488 | 843 | 103 | WNXA00000000 |
Diaporthe caulivora | D57 | Soybean | 97.8 | 57.8 | 52.9 | 18,385 | 1501 | ND | ND | ND |
Diaporthe citri | ZJUD2 | Citrus | 98.5 | 59.6 | 47.9 | 15,218 | 1860 | 847 | 98 | JADAZQ000000000 |
Diaporthe citriasiana | ZJUD30 | Citrus | 99.2 | 52.4 | 52.0 | 13,839 | 1643 | 796 | 89 | JADWDH000000000 |
Diaporthe citrichinensis | ZJUD34 | Citrus | 98.3 | 54.5 | 54.1 | 15,928 | 2043 | 925 | 110 | JADAZR000000000 |
Diaporthe eres (syn. D. vaccinii) | CBS 160.32 | Blueberry | 98.4 | 60.8 | 47.6 | 16,499 | 1616 | 859 | 88 | This study |
Diaporthe helianthi | DHEL01 | Sunflower | 98.3 | 63.6 | 43.9 | 13,139 | 1433 | 764 | 67 | MAVT02000001 |
Diaporthe longicolla | MSPL 10–6 | Soybean | 98.2 | 62.0 | 48.6 | 16,597 | 1535 | 1221 | 174 | AYRD00000000 |
Classes | Total Number of Genes | Secreted CAZymes | ||
---|---|---|---|---|
D. amygdali | D. eres | D. amygdali | D. eres | |
GT | 107 | 108 | 3 | 10 |
GH | 404 | 398 | 235 | 40 |
CBM | 20 | 25 | 11 | 4 |
AA | 230 | 225 | 131 | 26 |
CE | 63 | 66 | 44 | 5 |
PL | 33 | 37 | 30 | 3 |
TOTAL | 857 | 859 | 454 | 88 |
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Hilário, S.; Gonçalves, M.F.M.; Fidalgo, C.; Tacão, M.; Alves, A. Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32. J. Fungi 2022, 8, 804. https://doi.org/10.3390/jof8080804
Hilário S, Gonçalves MFM, Fidalgo C, Tacão M, Alves A. Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32. Journal of Fungi. 2022; 8(8):804. https://doi.org/10.3390/jof8080804
Chicago/Turabian StyleHilário, Sandra, Micael F. M. Gonçalves, Cátia Fidalgo, Marta Tacão, and Artur Alves. 2022. "Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32" Journal of Fungi 8, no. 8: 804. https://doi.org/10.3390/jof8080804