Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation of Bacteria and DNA Preparation
2.2. Genome Sequencing and Assembly
2.3. Genome Component Prediction and Gene Annotation
2.4. Average Nucleotide Identity and Phylogenetic Analysis
2.5. Comparative Genomic Analysis
3. Results
3.1. General Genomic Features of X. albilineans Strain Xa-FJ1
3.2. Functional Annotation of the Predicted Genes of X. albilineans Strain Xa-FJ1
3.3. Average Nucleotide Identity and Phylogenetic Analysis among Strains of X. albilineans
3.4. Chromosomal Structural Variation Between Strains Xa-FJ1 and GPE PC73 of X. albilineans
3.5. Chromosomal Specific Genes between Strain Xa-FJ1 and Strain GPE PC73 of X. albilineans
3.6. Genes Present in Plasmids, PlasmI and PlasmIII, of Strain GPE PC73 of X. albilineans from Guadeloupe and Absent in Strain Xa-FJ1 from China
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Element and Characteristics | Xa-FJ1 | GPE PC73 |
---|---|---|
Sequencing platform | PacBio RSII, Illumina PE150 | Sanger |
Coverage | 206×, 570× | 17× |
Size (bp) | 3,724,581 | 3,768,695 |
G + C content (%) | 63 | 63 |
No. protein-coding sequences (CDSs) | 3176 | 3115 |
Coding density (%) | 86.66 | 84 |
Average length in bp of all CDSs | 1016 | 1059 |
Region | Xa-FJ1 | GPE PC73 | Variation Type (Reference = Xa-FJ1) | Fragment Length (nt) | Predicted Cause of Variation | Affected Gene(s) | |||
---|---|---|---|---|---|---|---|---|---|
Begins | Ends | Begins | Ends | Xa-FJ1 | GPE PC73 | ||||
R1 | 219,400 | 219,400 | 219,691 | 271,791 | Insertion | 0 | 52,101 | Prophage integration | XALc_0171-XALc_0242 (72 specific genes in GPE PC73) |
R2 | 679,518 | 681,202 | 731,933 | 731,933 | Deletion | 1685 | 0 | Recombination/assembly defect | XaFJ1_GM000644; XaFJ1_GM000645; XaFJ1_GM000646 |
R3 | 1,165,743 | 1,168,928 | 1,216,465 | 1,216,465 | Deletion | 3186 | 0 | Recombination/assembly defect | XaFJ1_GM001035; XALc_1056 |
R4 | 1,727,177 | 1,727,177 | 1,774,582 | 1,780,815 | Insertion | 0 | 6234 | Recombination/assembly defect | XaFJ1_GM001510; XALc_1529 |
R5 | 1,736,246 | 1,736,755 | 1,789,885 | 1,790,986 | Complex Indel | 510 | 1102 | Prophage integration | XALC_1536-XALC_1545 (10 specific genes in GPE PC73); XaFJ1_GM001517-XaFJ1_GM001525 (9 specific genes in Xa-FJ1) |
R6 | 1,736,873 | 1,741,929 | 1,791,101 | 1,795,842 | Complex Indel | 5057 | 4742 | Prophage integration | |
R7 | 1,742,065 | 1,742,065 | 1,795,979 | 1,796,122 | Insertion | 0 | 144 | Prophage integration | |
R8 | 1,742,742 | 1,742,742 | 1,796,839 | 1,797,116 | Insertion | 0 | 278 | Prophage integration | |
R9 | 1,778,246 | 1,784,662 | 1,832,620 | 1,832,620 | Deletion | 6417 | 0 | Recombination/assembly defect | XaFJ1_GM001532; XALc_1551 |
R10 | 2,484,556 | 2,484,556 | 2,532,506 | 2,535,350 | Insertion | 0 | 2845 | Recombination/assembly defect | XaFJ1_GM002152; XALc_2151; XALc_2152 |
R11 | 26,75,326 | 2,679,992 | 2,726,120 | 2,726,120 | Deletion | 4667 | 0 | Transposable elements | XaFJ1_GM002293; XaFJ1_GM002292; XaFJ1_GM002291; XALc_2290 |
R12 | 3,041,680 | 3,041,680 | 3,087,815 | 3,088,684 | Insertion | 0 | 870 | Transposable elements | XALc_2603; XALc_2604 |
R13 | 3,377,378 | 3,377,378 | 3,424,367 | 3,424,696 | Insertion | 0 | 330 | CRISPR-Cas | Intergenic region which contains clustered regulatory interspaced short palindromic repeats |
R14 | 3,377,647 | 3,377,713 | 3,424,965 | 3,424,965 | Deletion | 67 | 0 | CRISPR-Cas | |
R15 | 3,377,912 | 3,377,912 | 3,425,163 | 3,425,227 | Insertion | 0 | 65 | CRISPR-Cas | |
R16 | 3,460,518 | 3,463,513 | 3,507,852 | 3,507,852 | Deletion | 2996 | 0 | Transposable elements | XaFJ1_GM002988; XaFJ1_GM002989; XaFJ1_GM002990; XALc_2969 |
Specific Gene | Annotation | Location |
---|---|---|
XaFJ1_GM001517 | zona occludens toxin | the plasticity zone, R5-R8 |
XaFJ1_GM001518 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM001519 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM001520 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM001521 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM001522 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM001523 | DNA-binding protein | the plasticity zone, R5-R8 |
XaFJ1_GM001524 | replication initiation protein | the plasticity zone, R5-R8 |
XaFJ1_GM001525 | hypothetical protein | the plasticity zone, R5-R8 |
XaFJ1_GM002989 | transposase | transposable elements, R16 |
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Zhang, H.-L.; Ntambo, M.S.; Rott, P.C.; Chen, G.; Chen, L.-L.; Huang, M.-T.; Gao, S.-J. Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms 2020, 8, 182. https://doi.org/10.3390/microorganisms8020182
Zhang H-L, Ntambo MS, Rott PC, Chen G, Chen L-L, Huang M-T, Gao S-J. Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms. 2020; 8(2):182. https://doi.org/10.3390/microorganisms8020182
Chicago/Turabian StyleZhang, Hui-Li, Mbuya Sylvain Ntambo, Philippe C. Rott, Gongyou Chen, Li-Lan Chen, Mei-Ting Huang, and San-Ji Gao. 2020. "Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald" Microorganisms 8, no. 2: 182. https://doi.org/10.3390/microorganisms8020182
APA StyleZhang, H. -L., Ntambo, M. S., Rott, P. C., Chen, G., Chen, L. -L., Huang, M. -T., & Gao, S. -J. (2020). Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms, 8(2), 182. https://doi.org/10.3390/microorganisms8020182