Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies
Abstract
:1. Introduction
2. Results
2.1. Binning of Single Microcystis Colony Metagenomes
2.2. Pipeline of Obtaining Genomes in Single Microcystis Colonies
2.3. Colony Classification and Sample Preparation
2.4. Mapping Results
2.5. Clustering Results
2.6. Assembly and Reads Binning
3. Discussion
4. Material and Methods
4.1. Sample Collection, Colony Classification, and Observation
4.2. Colony Lysis and DNA Amplification
4.3. Library Construction and Sequencing
4.4. Read Trimming, Alignment
4.5. Taxonomic Analysis and Clustering
4.6. De Novo Metagenome Assembly and Scaffold Coverage
4.7. Conserved Marker Genes Identification
4.8. Sequence Binning
4.9. Re-Assembly
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
MDA | multiple displacement amplification |
3D | three-dimension |
SEM | scanning electron microscope |
µcMDA | micro-channel MDA |
PBS | phosphate-buffered saline |
NCBI | National Center for Biotechnology Information |
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Aeruginosa-1 | Aeruginosa-2 | Wesenbergii-1 | Wesenbergii-2 | Panniformis-1 | Panniformis-2 | |
---|---|---|---|---|---|---|
Total reads (million) | 94.68 | 77.94 | 45.23 | 165.66 | 106.81 | 91.77 |
Coverage Ratio of NIES-843* | 67.87% | 69.71% | 83.83% | 78.41% | 80.56% | 75.70% |
Coverage Ratio of FACHB-1757 * | 68.20% | 70.35% | 87.09% | 94.30% | 99.89% | 95.32% |
Figure ID | No. Contigs | Total Length (bp) | GC (%) | No. Essential Genes | No. Duplicated Essential Genes | Standardized Relative Abundance* (%) | Genus | Phylogenetic Affiliation | |||
---|---|---|---|---|---|---|---|---|---|---|---|
aeruginosa | wesenbergii | panniformis | Overall | ||||||||
1 | 149 | 3,487,294 | 50.16 | 101/105 | 1 | 0.004 | 2.250 | 0.116 | 1.004 | Chryseolinea | Bacteroidetes |
2 | 309 | 4,301,792 | 42.03 | 102/106 | 5 | 0.190 | 0.528 | 0.095 | 0.443 | Pseudanabaena | Cyanobacteriaidetes |
3 | 3434 | 10,835,247 | 43.20 | 81/106 | 40 | 9.356 | 23.222 | 8.004 | 15.344 | Microcystis | Cyanobacteroidetes |
4 | 160 | 2,863,377 | 67.60 | 98/106 | 5 | 0.003 | 0.567 | 0.064 | 0.376 | Brevundimonas | Proteobacteria |
5 | 39 | 1,954,923 | 54.00 | 102/106 | 1 | 0.007 | 0.435 | 0.004 | 0.126 | Cupriavidus | Proteobacteria |
6 | 219 | 3,678,702 | 68.52 | 103/106 | 2 | 0.040 | 0.774 | 0.094 | 0.842 | Burkholderia | Proteobacteria |
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Tu, J.; Chen, L.; Gao, S.; Zhang, J.; Bi, C.; Tao, Y.; Lu, N.; Lu, Z. Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies. Int. J. Mol. Sci. 2019, 20, 5047. https://doi.org/10.3390/ijms20205047
Tu J, Chen L, Gao S, Zhang J, Bi C, Tao Y, Lu N, Lu Z. Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies. International Journal of Molecular Sciences. 2019; 20(20):5047. https://doi.org/10.3390/ijms20205047
Chicago/Turabian StyleTu, Jing, Liang Chen, Shen Gao, Junyi Zhang, Changwei Bi, Yuhan Tao, Na Lu, and Zuhong Lu. 2019. "Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies" International Journal of Molecular Sciences 20, no. 20: 5047. https://doi.org/10.3390/ijms20205047