Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens
Abstract
:1. Introduction
2. Methods
2.1. Sample Preparation
2.2. Illumina Whole-genome Sequencing
2.3. Data Analysis and Variant Detection
3. Results
3.1. Whole Genome Sequencing Analysis of D. melanogaster
Sample | # of reads | # of reads aligned | % reads aligned | Avg depth | # of SNVs | # of high quality SNVs | # of NS/SS cSNV | # of NS/SS cSNV on 3L | Unique NS/SS cSNV on 3L |
---|---|---|---|---|---|---|---|---|---|
Background | 42,278,410 | 37,650,186 | 88.1 | 27.1 | 412,362 | 88,593 | 21,745 | 2,851 | 25 |
Mutant 1 | 83,425,870 | 72,784,178 | 87.2 | 44.6 | 849,658 | 456,778 | 35,172 | 6,544 | 863 |
Mutant 2 | 43,972,798 | 38,172,143 | 86.81 | 23.4 | 647,655 | 427,332 | 25,054 | 5,252 | 533 |
Mutant 3 | 125,284,692 | 111,178,422 | 88.7 | 68.1 | 657,987 | 231,449 | 32,114 | 4,913 | 48 |
Total in Mutants | 2,155,300 | 1,115,559 | 92,340 | 16,709 | 1,444 |
Chromsome | Variants per Mbp |
---|---|
2L | 11023 |
2R | 9848 |
3L | 11043 |
3R | 8554 |
4 | 3331 |
X | 8108 |
Y | 72 |
3.2. Gene Identification Applying WGS
3.3. The Genomes Management Application (GEM.app)—A Novel Tool for Rapid Genome Analysis and Comparison
4. Discussion
- If a single mutant line exists, the parallel sequencing of the background strain and mapping to a chromosomal arm will reduce the number of genes carrying a strong coding variant to less than 20, possibly even identifying a strong mutation outright.
- It is most advantageous to add a second non-complementing strain to filter for genes that contain strong variants in both strains. In this case, further mapping of the gene is not even necessary in most cases (Figure 2).
- Adding more Drosophila genomes, related or unrelated to a project, has a great potential to further eliminate variants with a low frequency in the Drosophila population; or alternatively, nucleotide positions that are frequently hit by the EMS mutagen.
5. Conclusions
Acknowledgments
References
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Gonzalez, M.A.; Van Booven, D.; Hulme, W.; Ulloa, R.H.; Lebrigio, R.F.A.; Osterloh, J.; Logan, M.; Freeman, M.; Zuchner, S. Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens. Biology 2012, 1, 766-777. https://doi.org/10.3390/biology1030766
Gonzalez MA, Van Booven D, Hulme W, Ulloa RH, Lebrigio RFA, Osterloh J, Logan M, Freeman M, Zuchner S. Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens. Biology. 2012; 1(3):766-777. https://doi.org/10.3390/biology1030766
Chicago/Turabian StyleGonzalez, Michael A., Derek Van Booven, William Hulme, Rick H. Ulloa, Rafael F. Acosta Lebrigio, Jeannette Osterloh, Mary Logan, Marc Freeman, and Stephan Zuchner. 2012. "Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens" Biology 1, no. 3: 766-777. https://doi.org/10.3390/biology1030766
APA StyleGonzalez, M. A., Van Booven, D., Hulme, W., Ulloa, R. H., Lebrigio, R. F. A., Osterloh, J., Logan, M., Freeman, M., & Zuchner, S. (2012). Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens. Biology, 1(3), 766-777. https://doi.org/10.3390/biology1030766