Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome Data Curation
2.2. Metabolic Reconstruction
2.3. Phylogenetic Analysis
3. Results and Discussion
3.1. Genomic Benchmarks
3.2. Pan-Genome Analysis
3.3. Membrane Transport Proteins
3.4. Carbohydrate Metabolism
3.4.1. Sucrose Degradation
3.4.2. Glycolysis
3.4.3. Carboxylic Acid Metabolism
3.4.4. Acetogenesis
3.4.5. Glycerophospholipid Metabolism
3.4.6. Glycerol Degradation
3.5. Secretion of Effectors
3.6. Immunodominant Membrane Proteins
3.7. Whole-Genome Comparison
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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‘Candidatus Phytoplasma’ Species | ||||
---|---|---|---|---|
rubi | ziziphi | ziziphi | Vitis | |
Strain | RS | Jwb-nky | Hebei-2018 | CH |
Chromosome organisation | Circular | Circular | Circular | Circular |
Chromosome size [bp] | 762,251 | 750,803 | 764,108 | 654,223 |
G + C content [%] | 23.53 | 23.22 | 23.22 | 21.74 |
CDS | 887 | 671 | 710 | 508 |
CDS coding | 685 | 640 | 659 | 498 |
Hypothetical proteins | 242 | 308 | 256 | 138 |
rRNA operons | 2 | 2 | 2 | 2 |
tRNAs | 32 | 32 | 33 | 32 |
Plasmids | 0 | 0 | 0 | 0 |
Data source | CP114006.1 | CP025121.1 | NZ_CP091835.1 | CP097583.1 |
[32] | [30] | [31] | [29] | |
Data generated with automatic annotation pipeline (RAST) | ||||
Coding density [CDS/kb] | 1.163 | 0.957 | 1.029 | 0.816 |
average CDS length | 655 | 824 | 730 | 944 |
CDS (RAST) | 887 | 719 | 787 | 534 |
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Böhm, J.W.; Duckeck, D.; Duduk, B.; Schneider, B.; Kube, M. Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features. Appl. Microbiol. 2023, 3, 1083-1100. https://doi.org/10.3390/applmicrobiol3030075
Böhm JW, Duckeck D, Duduk B, Schneider B, Kube M. Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features. Applied Microbiology. 2023; 3(3):1083-1100. https://doi.org/10.3390/applmicrobiol3030075
Chicago/Turabian StyleBöhm, Jan Werner, Dominik Duckeck, Bojan Duduk, Bernd Schneider, and Michael Kube. 2023. "Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features" Applied Microbiology 3, no. 3: 1083-1100. https://doi.org/10.3390/applmicrobiol3030075