Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses
Abstract
:1. Introduction
2. Results
2.1. Flow Cytometry-Method Adaptation
2.2. Flow Cytometry—Analysis of Field Plants
2.3. Illumina Sequencing
2.4. K-Mer Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. Flow Cytometry Analyses
4.3. DNA Extraction, PCR Amplification and Sequencing
4.4. K-Mer Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
References
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Raw Sequencing Data | Quality Processed Sequencing Data | |||
---|---|---|---|---|
MiSeq | # read pairs | read length (bp) | # read pairs | read length (bp) |
Flow cell 1 | 455045310 | 119 | 446988504 | 120 |
Flow cell 2 | 153531660 | 119 | 150862318 | 120 |
HiSeq | # read pairs | read length (bp) | # read pairs | read length (bp) |
Lane 1 | 284728634 | 120 | 278778534 | 120 |
Lane 2 | 299563658 | 119 | 292564436 | 120 |
Lane 3 | 311852326 | 119 | 227020170 | 118 |
Lane 4 | 355362948 | 119 | 347367568 | 120 |
Lane 5 | 374476482 | 119 | 366378088 | 120 |
Lane 6 | 321173550 | 119 | 314166814 | 120 |
K19 | K23 | K27 | K47 | |||||||
---|---|---|---|---|---|---|---|---|---|---|
MiSEQ (0.6 Billion read pairs) | Raw | QP | Raw | QP | Raw | QP | Raw | QP | Average | SD |
GenomeScope v1 (CovMax 1k) | 0.60 | 0.60 | 0.64 | 0.64 | 0.67 | 0.67 | 0.74 | 0.75 | 0.66 | 0.06 |
GenomeScope v2 (CovMax 1k) | 0.59 | 0.59 | 0.63 | 0.63 | 0.66 | 0.66 | 0.74 | 0.74 | 0.66 | 0.06 |
GenomeScope v1 (CovMax 10k) | 0.76 | 0.76 | 0.79 | 0.79 | 0.81 | 0.81 | 0.84 | 0.85 | 0.80 | 0.03 |
GenomeScope v2 (CovMax 10k) | 0.76 | 0.76 | 0.79 | 0.79 | 0.80 | 0.80 | 0.83 | 0.84 | 0.80 | 0.03 |
GenomeScope v1 (CovMax 900k) | 0.97 | 0.97 | 0.97 | 0.97 | 0.97 | 0.97 | 0.95 | 0.95 | 0.97 | 0.01 |
GenomeScope v2 (CovMax 900k) | 0.97 | 0.96 | 0.97 | 0.96 | 0.96 | 0.96 | 0.94 | 0.94 | 0.96 | 0.01 |
FindGSE | 1.05 | 1.06 | 1.08 | 1.06 | 1.08 | 1.09 | 1.13 | 1.11 | 1.08 | 0.03 |
BBNorm | 1.05 | 1.06 | 1.08 | 1.06 | 1.08 | 1.09 | 1.14 | 1.13 | 1.09 | 0.03 |
Formula | 1.07 | 1.03 | 0.98 | 0.97 | 1.08 | 1.06 | 1.01 | 1.02 | 1.03 | 0.04 |
MiSEQ + HiSEQ (1.9 Billion read pairs) | Raw | QP | Raw | QP | Raw | QP | Raw | QP | Average | SD |
GenomeScope v1 (CovMax 1k) | 0.59 | 0.52 | 0.59 | 0.58 | 0.63 | 0.62 | 0.74 | 0.74 | 0.62 | 0.08 |
GenomeScope v2 (CovMax 1k) | 0.58 | 0.51 | 0.58 | 0.56 | 0.61 | 0.60 | 0.73 | 0.73 | 0.61 | 0.08 |
GenomeScope v1 (CovMax 10k) | 0.71 | 0.69 | 0.75 | 0.74 | 0.78 | 0.77 | 0.85 | 0.85 | 0.77 | 0.06 |
GenomeScope v2 (CovMax 10k) | 0.70 | 0.69 | 0.74 | 0.72 | 0.76 | 0.75 | 0.84 | 0.83 | 0.76 | 0.06 |
GenomeScope v1 (CovMax 900k) | 1.00 | 0.97 | 1.01 | 0.97 | 1.01 | 0.98 | 1.00 | 0.97 | 0.99 | 0.02 |
GenomeScope v2 (CovMax 900k) | 1.00 | 0.96 | 0.99 | 0.96 | 0.99 | 0.96 | 0.99 | 0.96 | 0.98 | 0.02 |
FindGSE | 1.01 | 1.04 | 1.01 | 1.04 | 1.01 | 1.05 | 1.04 | 1.06 | 1.03 | 0.02 |
BBNorm | 1.07 | 1.04 | 1.08 | 1.04 | 1.08 | 1.05 | 1.11 | 1.07 | 1.07 | 0.02 |
Formula | 1.07 | 1.02 | 1.06 | 1.01 | 1.06 | 1.02 | 1.00 | 0.97 | 1.03 | 0.03 |
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Mgwatyu, Y.; Stander, A.A.; Ferreira, S.; Williams, W.; Hesse, U. Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses. Plants 2020, 9, 270. https://doi.org/10.3390/plants9020270
Mgwatyu Y, Stander AA, Ferreira S, Williams W, Hesse U. Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses. Plants. 2020; 9(2):270. https://doi.org/10.3390/plants9020270
Chicago/Turabian StyleMgwatyu, Yamkela, Allison Anne Stander, Stephan Ferreira, Wesley Williams, and Uljana Hesse. 2020. "Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses" Plants 9, no. 2: 270. https://doi.org/10.3390/plants9020270
APA StyleMgwatyu, Y., Stander, A. A., Ferreira, S., Williams, W., & Hesse, U. (2020). Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses. Plants, 9(2), 270. https://doi.org/10.3390/plants9020270