Improving the Comprehension of Pathogenicity and Phylogeny in ‘Candidatus Phytoplasma meliae’ through Genome Characterization
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Samples
2.2. Library Construction and Sequencing
2.3. Assembly and Annotation
2.4. Identification of Putative Effector Proteins
2.5. PMU Core Gene and Intact PMU Identification
2.6. Ortholog Clustering and Phylogenetic Analyses
3. Results and Discussion
3.1. Assembly and Key Features of the Draft Genome of ‘Ca. Phytoplasma meliae’
3.2. Metabolic Pathways
3.3. Secreted Protein Identification Revealed a Unique Effectors Repertoire
3.4. PMU Identification
3.5. Phylogenomic Analysis and Taxonomic Delineation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Ca. meliae | Ca. hispanicum | Ca. Solani | Ca. australiense | Ca. asteris | |
---|---|---|---|---|---|
Features/Strain | ChTYXIII | StrPh-CL | SA-1 | PAa | AYWB |
# Contigs | 21 | 33 | 19 | 1 | 1 |
Total Length (bp) | 751.949 | 627.584 | 821.322 | 879.324 | 706.569 |
G + C content (%) | 27.31 | 25.40 | 28.30 | 27.00 | 27.00 |
N(50) | 53.850 | 82.058 | 76.256 | - | - |
Assembly status | draft | draft | draft | complete | complete |
Total CDSs | 669 | 559 | 709 | 839 | 671 |
CDSs w-function | 472 | 440 | 452 | 502 | 450 |
CDSs h-protein | 197 | 119 | 257 | 337 | 221 |
rRNA-operons | 1 | 2 | 2 | 2 | 2 |
tRNA | 34 | 32 | 32 | 35 | 32 |
BUSCO | 94.70% | 93.40% | 95.40% | 94.70% | 93.40% |
Genbank # | JACAOD000000000.2 | JAGVRH000000000.1 | MPBG01000000.1 | AM422018.1 | CP000061.1 |
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Fernández, F.D.; Yan, X.-H.; Kuo, C.-H.; Marcone, C.; Conci, L.R. Improving the Comprehension of Pathogenicity and Phylogeny in ‘Candidatus Phytoplasma meliae’ through Genome Characterization. Microorganisms 2024, 12, 142. https://doi.org/10.3390/microorganisms12010142
Fernández FD, Yan X-H, Kuo C-H, Marcone C, Conci LR. Improving the Comprehension of Pathogenicity and Phylogeny in ‘Candidatus Phytoplasma meliae’ through Genome Characterization. Microorganisms. 2024; 12(1):142. https://doi.org/10.3390/microorganisms12010142
Chicago/Turabian StyleFernández, Franco Daniel, Xiao-Hua Yan, Chih-Horng Kuo, Carmine Marcone, and Luis Rogelio Conci. 2024. "Improving the Comprehension of Pathogenicity and Phylogeny in ‘Candidatus Phytoplasma meliae’ through Genome Characterization" Microorganisms 12, no. 1: 142. https://doi.org/10.3390/microorganisms12010142
APA StyleFernández, F. D., Yan, X.-H., Kuo, C.-H., Marcone, C., & Conci, L. R. (2024). Improving the Comprehension of Pathogenicity and Phylogeny in ‘Candidatus Phytoplasma meliae’ through Genome Characterization. Microorganisms, 12(1), 142. https://doi.org/10.3390/microorganisms12010142