Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture
Abstract
:1. Introduction
2. Results
2.1. Strain Isolation and Identification
2.2. Genome Sequencing and Analysis
2.2.1. Genome Properties
2.2.2. Radiation Resistance Genes and Pathways
2.2.3. Genes Involved in Plant Growth
2.3. Radiation-Resistance Analysis
2.4. Plant-Growth Analysis
3. Discussion
4. Materials and Methods
4.1. Isolation and Growth
4.2. Genome Sequencing and Phylogenomic Analysis
4.3. Genome Annotation
4.4. Radiation Resistant Analysis
4.4.1. γ Irradiation Analysis
4.4.2. UVC Irradiation Analysis
4.5. Plant Growth Analysis
Plant Cultivation and Treatments
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Features | Chromosome | Plasmid 1 | Plasmid 2 | Plasmid 3 |
---|---|---|---|---|
Strain | ES10-3-2-2 | ES10-3-2-2 | ES10-3-2-2 | ES10-3-2-2 |
Number of contigs | 1 | 1 | 1 | 1 |
GenBank Accession No. | CP015317 | CP155472 | CP155473 | CP155474 |
Chromosome size (pb) | 6,408,035 | 212,574 | 175,683 | 81,564 |
GC content | 52.8 | 52.4 | 49.0 | 52.9 |
Sequencing coverage | 71 | 71 | 71 | 71 |
Genes | 5252 | 189 | 159 | 91 |
rRNA | 9 | 0 | 0 | 0 |
5s rRNAs | 3 | 0 | 0 | 0 |
16S rRNAs | 3 | 0 | 0 | 0 |
23S rRNA | 3 | 0 | 0 | 0 |
tRNAs | 43 | 0 | 0 | 0 |
ncRNAs | 2 | 0 | 0 | 0 |
Pseudo genes | 45 | 0 | 0 | 0 |
S. No. | Length | Function | Sequence Similarity (BLAST) | |
---|---|---|---|---|
D. radiodurans R1 | E. coli K12 | |||
1 | 999 | Excinuclease ABC subunit A paralog | 39.2 | 44.2 |
2 | 977 | Excinuclease ABC subunit A | 51.8 | 51.9 |
3 | 767 | ATP-dependent DNA helicase UvrD/PcrA | 37.5 | 37.2 |
4 | 674 | Excinuclease ABC subunit B | 50.0 | 54.8 |
5 | 605 | Excinuclease ABC subunit C | 31.1 | 33.4 |
6 | 845 | Excinuclease ABC subunit A paralog | 71.3 | 40.3 |
7 | 690 | DNA ligase (NAD (+)) | 34.4 | 40.6 |
8 | 886 | Excinuclease ABC subunit A paralog of unknown function | 63.5 | 38.0 |
S. No. | Length | Function | Sequence Similarity (BLAST) | |
---|---|---|---|---|
D. radiodurans R1 | E. coli K12 | |||
1 | 703 | ATP-dependent DNA helicase RecG | 41.1 | 40.0 |
2 | 193 | Crossover junction endodeoxyribonuclease RuvC | 38.6 | 36.8 |
3 | 365 | DNA recombination and repair protein RecF | 26.3 | 26.4 |
4 | 231 | DNA recombination and repair protein RecO | 0.0 | 0.0 |
5 | 459 | DNA repair protein RadA | 42.9 | 46.0 |
6 | 555 | DNA repair protein RecN | 30.7 | 29.8 |
7 | 1029 | Exonuclease SbcC | 34.8 | 50.0 |
8 | 418 | Exonuclease SbcD | 32.3 | 32.5 |
9 | 836 | Helicase PriA essential for oriC/DnaA | 36.6 | 37.6 |
10 | 196 | Holliday junction ATP-dependent DNA helicase RuvA | 33.5 | 39.7 |
11 | 343 | Holliday junction ATP-dependent DNA helicase RuvB | 54.4 | 59.3 |
12 | 363 | RecA protein | 59.2 | 59.8 |
13 | 206 | Recombination protein RecR | 45.8 | 40.4 |
14 | 590 | Single-stranded, DNA-specific exonuclease RecJ | 32.2 | 31.6 |
KEGG Map | Distinct ECs | Strain ES10-3-2-2 | “F. algicola JA-25” | Fibrella aestuarina BUZ 2T | Spirosoma linguale SM 74T |
---|---|---|---|---|---|
Biosynthesis of plant hormones | 131 | 66 (50.4%) | 66 (50.4%) | 76 (58.0%) | 75 (57.3%) |
Brassinosteroid biosynthesis | 3 | 1 (33.3%) | 1 (33.3%) | 2 (66.7%) | 2 (66.7%) |
Fatty acid biosynthesis | 21 | 10 (47.6%) | 10 (47.6%) | 10 (47.6%) | 12 (57.1%) |
Terpenoid backbone biosynthesis | 27 | 10 (37.0%) | 10 (37.0%) | 15 (55.6%) | 14 (51.9%) |
Zeatin biosynthesis | 9 | 0 | 0 | 0 | 0 |
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Srinivasan, S. Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture. Genes 2024, 15, 1048. https://doi.org/10.3390/genes15081048
Srinivasan S. Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture. Genes. 2024; 15(8):1048. https://doi.org/10.3390/genes15081048
Chicago/Turabian StyleSrinivasan, Sathiyaraj. 2024. "Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture" Genes 15, no. 8: 1048. https://doi.org/10.3390/genes15081048