Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. TnpB-Containing Mobile Elements Mining
2.2. Sequence Analysis and Phylogenetic Tree Construction
2.3. Hairpin Structures Prediction
3. Results
3.1. Distribution of TnpB-Containing Mobile Elements (TCMEs) in the Six Species of Bacteria
3.2. Protein Type and Structure Organization of TCMEs in Six Species
3.3. Domains and Phylogenetic Analysis of Y1, SR, and TnpB
3.4. Differential Distribution of TCMEs in the Genomes of Six Species
4. Discussion
4.1. Co-Evolution Profiles of TnpB, an RNA-Guided Endonuclease, with Y1 and SR
4.2. Structure Organization of TCMEs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Genomes Detected | Detected Elements | TCMEs | Genome Number Contain TCMEs/% a | Average Copy Number of TCMEs in Each Genome | Copy Number of Full TCMEs/% b |
---|---|---|---|---|---|---|
B. cereus | 152 | 687 | 687 | 126/83% | 5.28 ± 3.73 | 520/76% |
C. difficile | 133 | 1875 | 1875 | 132/99% | 14.15 ± 6.82 | 1760/93% |
D. radiodurans | 12 | 52 | 44 | 12/100% | 3.67 ± 1.65 | 44/100% |
E. coli | 2467 | 4837 | 4825 | 2325/94% | 2.05 ± 0.94 | 4412/91% |
H. pylori | 335 | 735 | 734 | 214/64% | 3.43 ± 2.99 | 678/92% |
S. enterica | 1495 | 1875 | 1831 | 658/44% | 1.25 ± 0.61 | 757/41% |
Species | Total Genomes Detected | Genomes Number Containing IS605/% d | Genomes Number Containing IS607/% d | Genomes Contain IS134 d | |||||
---|---|---|---|---|---|---|---|---|---|
IS605a | IS605b | IS605c | Total | IS607a | IS607b | Total | IS1341 | ||
B. cereus | 152 | 0 | 82/53.95 | 0 | 82/53.95 | 39/25.66 | 12/7.89 | 48/31.58 | 112/73.68 |
C. difficile | 133 | 56/42.11 | 132/99.25 | 0 | 132/99.25 | 0 | 15/11.28 | 15/11.28 | 106/79.70 |
D. radiodurans | 12 | 12/100 | 0 | 0 | 12/100 | 0 | 0 | 0 | 0 |
E. coli | 2467 | 0 | 0 | 2242/90.88 | 2242/90.88 | 0 | 0 | 0 | 312/12.65 |
H. pylori | 335 | 58/17.31 | 0 | 123/36.72 | 177/52.84 | 81/24.18 | 0 | 81/24.18 | 0 |
S. enterica | 1495 | 0 | 0 | 303/20.27 | 303/20.27 | 0 | 0 | 0 | 418/27.96 |
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Wang, Y.; Guo, M.; Yang, N.; Guan, Z.; Wu, H.; Ullah, N.; Asare, E.; Shi, S.; Gao, B.; Song, C. Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes 2023, 14, 523. https://doi.org/10.3390/genes14020523
Wang Y, Guo M, Yang N, Guan Z, Wu H, Ullah N, Asare E, Shi S, Gao B, Song C. Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes. 2023; 14(2):523. https://doi.org/10.3390/genes14020523
Chicago/Turabian StyleWang, Yali, Mengke Guo, Naisu Yang, Zhongxia Guan, Han Wu, Numan Ullah, Emmanuel Asare, Shasha Shi, Bo Gao, and Chengyi Song. 2023. "Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species" Genes 14, no. 2: 523. https://doi.org/10.3390/genes14020523