Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil
Abstract
:1. Introduction
2. Materials and Methods
2.1. Salmonella Isolation
2.2. DNA Isolation
2.3. Amplification of 16S rRNA Gene
2.4. 16S rRNA Gene Sequencing and Phylogenetic Analysis
2.5. Whole Genome Sequencing (WGS) by MinION and Illumina
2.6. Hybrid Genome Sequence Assembly
2.7. Serotype Identification
2.8. Gene Annotation
2.9. Genome Similarity Assessment
2.10. Pangenome Analysis
2.11. Mobile Genetic Element Identification and Annotation
3. Results
3.1. Salmonella Isolation and Characterization
3.2. Analysis of 16S rRNA
3.3. Whole Genome Sequencing of Salmonella Isolate SE3
3.4. Genome Assembly
3.5. Completeness of the Genome Annotation
3.6. Genomic Relatedness of Salmonella SE3
3.7. Pangenome Analysis
3.8. Genome Features
3.8.1. Resistome Identification
3.8.2. Viriome, Genomic Island and Pathogenic Island Identification
3.9. Identification of Antiviral Defense Systems
3.10. Prophage Identification
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sequence Data | HiSeq | MinION |
---|---|---|
Reads | 15,997,283 | 13,326 |
Total read bases (bp) | 7,999,481 | 67,978,671 |
Mean coverage (%) | 51,185 | 13,590 |
Longest read (bp) | 151 | 28,841 |
Mean read length (bp) | 150 | 5101 |
GC % | 52.00 | 52.18 |
Genome size (bp) | 4,688,543 | 4,709,033 |
Assembly Method | Racon | Unicycler | Edena | SPAdes | Unicycler | MaSuRCA |
---|---|---|---|---|---|---|
Sequence data | MinION | HiSeq | HiSeq | HiSeq | Hybrid | Hybrid |
Number of contigs | 2 | 31 | 41 | 50 | 10 | 39 |
Number of contigs (≥0 bp) | 2 | 65 | 54 | 111 | 18 | 42 |
Number of contigs (≥50 kb) | 2 | 15 | 4,475,114 | 4,566,140 | 4 | 24 |
Largest contigs | 4,671,311 | 1,262,086 | 488,615 | 1,276,166 | 2,750,500 | 519,108 |
Total length (≥50 kb) | 4,730,597 | 4,683,367 | 4,701,851 | 4,805,245 | 4,713,463 | 4,585,719 |
GC (%) | 52.18 | 52.14 | 52.15 | 51.85 | 52.16 | 52.15 |
N50 | 4,671,311 | 478,501 | 181,604 | 491,607 | 2,750,500 | 246,991 |
L50 | 1 | 3 | 8 | 3 | 1 | 7 |
Assembly Method | Sequence Data | Complete (%) | Single Copy (%) | Duplicated (%) | Fragmented (%) | Missing (%) |
---|---|---|---|---|---|---|
Racon | MinION | 74.2 | 74.2 | 0 | 19.4 | 6.4 |
Unicycler | HiSeq | 98.4 | 98.4 | 0 | 0 | 1.64 |
Unicycler | Hybrid | 98.4 | 98.4 | 0 | 0 | 1.64 |
MaSuRCA | Hybrid | 98.4 | 97.6 | 0.8 | 0 | 1.64 |
Annotated Genome | Features |
---|---|
rRNA | 20 |
tRNA | 87 |
Repeat region | 2 |
CDS | 4403 |
mRNA | 1 |
No | SPI | Identity | Query/Template Length | Salmonella Serotype | Insertion Site | Accession Number |
---|---|---|---|---|---|---|
1 | SPI-1 | 99.7 | 2705/2705 | Typhimurium SL1344 | fhlA/mutS | AF148689 |
2 | SPI-2 | 100 | 642/642 | Gallinarum SGC_2 | tRNA-valV | AY956827 |
3 | SPI-3 | 99.05 | 738/738 | Typhimurium 14028s | tRNA-selC | AJ000509 |
4 | SPI-5 | 99.11 | 9069/9069 | Typhimurium LT2 | tRNA-serT | NC_003197 |
5 | SPI-10 | 98.28 | 553/554 | Gallinarum SGE_3 | Unpublished | AY956839 |
6 | SPI-11 | 98.54 | 9085/15686 | Choleraesuis SC_B67 | Gifsy-1 | NC_006905 |
7 | SPI-12 | 97.14 | 5766/11075 | Choleraesuis SC_B67 | tRNA-pro | NC_006905 |
8 | SPI-13 | 100 | 341/341 | Gallinarum SGA_10 | tRNA-pheV | AY956834 |
9 | SPI-14 | 99.8 | 501/501 | Gallinarum SGA_8 | Unpublished | AY956835 |
10 | C63PI | 99.12 | 4000/4000 | Typhimurium SL1344 | fhlA | AF128999 |
11 | CS54 | 98.09 | 19669/25252 | Typhimurium ATCC_14028 | xseA-yfgK | AF140550 |
12 | Unnamed | 100 | 330/330 | Enteritidis CMCC50041 | -- | JQ071613 |
Number | System | Subtype | Tool | Reference |
---|---|---|---|---|
1 | AbiU | AbiU | PADLOC | [46] |
2 | Cas type IE | Cas3e | PADLOC | [46] |
3 | Cas type IE | Cas8e | PADLOC | [46] |
4 | Cas type IE | Cas11e | PADLOC | [46] |
5 | Cas type IE | Cas7e | PADLOC | [46] |
6 | Cas type IE | Cas5e | PADLOC | [46] |
7 | Cas type IE | Cas6e | PADLOC | [46] |
8 | Cas type IE | Cas1e | PADLOC | [46] |
9 | Cas type IE | Cas2e | PADLOC | [46] |
10 | CBASS_type_I | Cyclase | PADLOC | [46] |
11 | CBASS_type_I | Effector | PADLOC | [46] |
12 | CRISPR array | CRISPR array | PADLOC | [46] |
13 | CRISPR array | CRISPR array | PADLOC | [46] |
14 | RM type I | Mtase I | PADLOC | [46] |
15 | RM type I | Specificity I | PADLOC | [46] |
16 | RM type I | Rease I | PADLOC | [46] |
17 | RM type II | Rease II | PADLOC | [46] |
18 | RM type II | Mtase II | PADLOC | [46] |
19 | RM type III | Rease III | PADLOC | [46] |
20 | RM type III | Mtase III | PADLOC | [46] |
21 | Cas Class1 subtype I E1 | Cas3 I 5 | DefenseFinder | [47] |
22 | Cas Class1 subtype I E1 | Cas8e I E 1 | DefenseFinder | [47] |
23 | Cas Class1 subtype I E1 | Cas2gr11 I E 2 | DefenseFinder | [47] |
24 | Cas Class1 subtype I E1 | Cas7 I E 2 | DefenseFinder | [47] |
25 | Cas Class1 subtype I E1 | Cas5 I E 3 | DefenseFinder | [47] |
26 | Cas Class1 subtype I E1 | Cas6e I II II IV V VI 1 | DefenseFinder | [47] |
27 | Cas Class1 subtype I E1 | Cas 1 I E 1 | DefenseFinder | [47] |
28 | Cas Class1 subtype I E1 | Cas2 I E 2 | DefenseFinder | [47] |
29 | CBASS I 2 | Cyclase SMODS | DefenseFinder | [47] |
30 | CBASS I 2 | 2TM Gros | DefenseFinder | [47] |
31 | RM Type III 2 | Type III Reases | DefenseFinder | [47] |
32 | RM Type III 2 | Type III Mtases | DefenseFinder | [47] |
33 | RM Type I 1 | Type I S | DefenseFinder | [47] |
34 | RM Type I 1 | Type I Mtases | DefenseFinder | [47] |
35 | RM Type I 1 | Type I S | DefenseFinder | [47] |
36 | RM Type I 1 | Type I Reases | DefenseFinder | [47] |
Completeness | Score | Proteins | Position | Best Match | Accession No. | GC (%) |
---|---|---|---|---|---|---|
Incomplete | 60 | 27 | 805989–831780 | Shigella phage POCJ13 | NC_025434 | 48.7 |
Intact | 150 | 40 | 1041034–1072153 | Salmonella phage Gifsy-2 | NC_010393 | 47.2 |
Incomplete | 50 | 13 | 1276587–1286489 | Salmonella phage Gifsy-2 | NC_010393 | 46.7 |
Incomplete | 30 | 9 | 1698977–1705339 | Shigella phage POCJ13 | NC_025434 | 45.6 |
Intact | 150 | 49 | 1081056–1124788 | Salmonella phage RE-2010 | NC_019488 | 51.2 |
Incomplete | 20 | 8 | 1435195–1442595 | Escherichia phage 500465-2 | NC_049343 | 53.2 |
Incomplete | 40 | 9 | 29216–37324 | Salmonella phage RE-2010 | NC_019488 | 52.4 |
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Romero-Calle, D.X.; Pedrosa-Silva, F.; Tomé, L.M.R.; Sousa, T.J.; de Oliveira Santos, L.T.S.; de Carvalho Azevedo, V.A.; Brenig, B.; Benevides, R.G.; Venancio, T.M.; Billington, C.; et al. Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil. Microorganisms 2023, 11, 111. https://doi.org/10.3390/microorganisms11010111
Romero-Calle DX, Pedrosa-Silva F, Tomé LMR, Sousa TJ, de Oliveira Santos LTS, de Carvalho Azevedo VA, Brenig B, Benevides RG, Venancio TM, Billington C, et al. Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil. Microorganisms. 2023; 11(1):111. https://doi.org/10.3390/microorganisms11010111
Chicago/Turabian StyleRomero-Calle, Danitza Xiomara, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tomé, Thiago J. Sousa, Leila Thaise Santana de Oliveira Santos, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Raquel Guimarães Benevides, Thiago M. Venancio, Craig Billington, and et al. 2023. "Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil" Microorganisms 11, no. 1: 111. https://doi.org/10.3390/microorganisms11010111
APA StyleRomero-Calle, D. X., Pedrosa-Silva, F., Tomé, L. M. R., Sousa, T. J., de Oliveira Santos, L. T. S., de Carvalho Azevedo, V. A., Brenig, B., Benevides, R. G., Venancio, T. M., Billington, C., & Góes-Neto, A. (2023). Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil. Microorganisms, 11(1), 111. https://doi.org/10.3390/microorganisms11010111