Takeaways from Mobile DNA Barcoding with BentoLab and MinION
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Illumina NGS Barcoding as Reference
2.3. Laboratory BentoLab Extraction and Amplification
2.4. Field Sequencing with BentoLab and MinION
2.5. MinION Bioinformatics
2.6. Assessing MinION Barcode Accuracy and Quality
3. Results
3.1. Marine Faunal Diversity
3.2. Gene Amplification
3.3. Barcode Calling
3.4. MinION Barcode Assessment
3.5. DNA Barcodes and Species Diversity
4. Discussion
4.1. Takeaway #1: Portability and Productivity
4.2. Takeaway #2: Operational Costs
4.3. Takeaway #3: Flow Cell Chemistry and Basecalling Model
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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R9.4.1_Fast | R9.4.1_HAC | R10.3_Fast_ST | R10.3_HAC_ST | R10.3_Fast_SR | R10.3_HAC_SR | |
---|---|---|---|---|---|---|
Basecalled reads | 1,056,403 | 1,056,403 | 512,000 | 512,000 | 1,060,000 | 1,060,000 |
Demultiplexed (%) | 115,833 (11.0) | 161,376 (15.3) | 50,203 (9.8) | 109,955 (21.5) | 121,579 (11.5) | 264,501 (25.0) |
Read depth per sample | 11–36,925 | 11–49,990 | 10–2517 | 11–5086 | 10–6037 | 10–12,221 |
MAFFT / <1% Ns-filter | 125/101 | 126/111 | 115/92 | 121/114 | 122/101 | 128/117 |
RACON | 101 | 111 | 92 | 114 | 101 | 117 |
MAFFT+AA | 97 | 110 | 90 | 113 | 99 | 115 |
RACON+AA | 98 | 110 | 91 | 113 | 100 | 115 |
Consolidated | 86 | 104 | 83 | 111 | 92 | 113 |
Consolidated (Clean) | 79 | 96 | 75 | 102 | 84 | 103 |
R9.4.1_Fast | R9.4.1_HAC | R10.3_Fast_ST | R10.3_HAC_ST | R10.3_Fast_SR | R10.3_HAC_SR | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Barcode | N | G | A (%) | N | G | A (%) | N | G | A (%) | N | G | A (%) | N | G | A (%) | N | G | A (%) |
MAFFT Ns-filter | 65 | 198 | 99.9800 | 74 | 99 | 100.0000 | 62 | 202 | 99.9843 | 76 | 31 | 99.9958 | 69 | 233 | 99.9812 | 77 | 33 | 100.0000 |
RACON | 65 | 119 | 99.9801 | 74 | 50 | 100.0000 | 62 | 121 | 99.9480 | 76 | 7 | 100.0000 | 69 | 125 | 99.9673 | 77 | 9 | 99.9834 |
MAFFT+AA (namino1) | 62 | 0 | 99.9428 | 73 | 1 | 99.9516 | 61 | 0 | 99.9315 | 75 | 0 | 99.9914 | 68 | 4 | 99.9149 | 76 | 0 | 99.9916 |
MAFFT+AA (namino2) | 62 | 0 | 99.9479 | 73 | 1 | 99.9736 | 61 | 0 | 99.9525 | 75 | 0 | 99.9957 | 68 | 2 | 99.9479 | 76 | 0 | 100.0000 |
MAFFT+AA (namino3) | 62 | 2 | 99.9791 | 73 | 1 | 99.9780 | 61 | 0 | 99.9524 | 75 | 0 | 99.9957 | 68 | 4 | 99.9668 | 76 | 0 | 100.0000 |
RACON+AA (namino1) | 63 | 1 | 99.9387 | 73 | 0 | 99.9780 | 61 | 4 | 99.8735 | 75 | 0 | 99.9914 | 68 | 0 | 99.9339 | 76 | 0 | 99.9620 |
RACON+AA (namino2) | 63 | 1 | 99.9488 | 73 | 0 | 99.9912 | 61 | 4 | 99.9101 | 75 | 0 | 100.0000 | 68 | 0 | 99.9479 | 76 | 0 | 99.9831 |
RACON+AA (namino3) | 63 | 1 | 99.9589 | 73 | 0 | 99.9912 | 61 | 5 | 99.9204 | 75 | 0 | 100.0000 | 68 | 0 | 99.9525 | 76 | 0 | 99.9831 |
Consolidated (namino1) | 55 | 0 | 99.9532 | 70 | 0 | 99.9679 | 58 | 0 | 99.9003 | 73 | 0 | 99.9912 | 64 | 0 | 99.9599 | 74 | 0 | 99.9913 |
Consolidated (namino2) | 55 | 0 | 99.9648 | 70 | 0 | 99.9862 | 58 | 0 | 99.9223 | 73 | 0 | 99.9956 | 64 | 0 | 99.9649 | 74 | 0 | 100.0000 |
Consolidated (namino3) | 55 | 0 | 99.9707 | 70 | 0 | 99.9862 | 58 | 0 | 99.9333 | 73 | 0 | 99.9956 | 64 | 0 | 99.9648 | 74 | 0 | 100.0000 |
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Chang, J.J.M.; Ip, Y.C.A.; Ng, C.S.L.; Huang, D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes 2020, 11, 1121. https://doi.org/10.3390/genes11101121
Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes. 2020; 11(10):1121. https://doi.org/10.3390/genes11101121
Chicago/Turabian StyleChang, Jia Jin Marc, Yin Cheong Aden Ip, Chin Soon Lionel Ng, and Danwei Huang. 2020. "Takeaways from Mobile DNA Barcoding with BentoLab and MinION" Genes 11, no. 10: 1121. https://doi.org/10.3390/genes11101121
APA StyleChang, J. J. M., Ip, Y. C. A., Ng, C. S. L., & Huang, D. (2020). Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes, 11(10), 1121. https://doi.org/10.3390/genes11101121