Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)
Abstract
:1. Introduction
2. Results
2.1. Sequence Characteristics
Subgenus | Barcode Region | N Individuals | N Species | N Singletons | Alignment Length (bp) | Variable Characters(%) | PI Characters (%) | Overall K2P (%) |
---|---|---|---|---|---|---|---|---|
Astrophea | ITS1 | 53 | 16 | 12 | 291 | 32.99 | 22.68 | 8.8 |
ITS2 | 53 | 16 | 12 | 237 | 28.27 | 16.46 | 7.2 | |
ITS1+2 | 53 | 16 | 12 | 528 | 30.87 | 19.89 | 8.0 | |
Decaloba | ITS1 | 314 | 134 | 85 | 359 | 76.88 | 65.46 | 24.7 |
ITS2 | 314 | 134 | 85 | 258 | 72.87 | 56.59 | 14.0 | |
ITS1+2 | 314 | 134 | 85 | 617 | 75.20 | 61.75 | 19.7 | |
Deidamioides | ITS1 | 101 | 8 | 3 | 301 | 40.53 | 24.92 | 4.8 |
ITS2 | 101 | 8 | 3 | 226 | 44.25 | 25.22 | 5.8 | |
ITS1+2 | 101 | 8 | 3 | 527 | 42.13 | 25.05 | 5.3 | |
Passiflora | ITS1 | 287 | 64 | 46 | 292 | 55.48 | 39.73 | 8.8 |
ITS2 | 287 | 64 | 46 | 249 | 52.21 | 30.92 | 3.8 | |
ITS1+2 | 287 | 64 | 46 | 541 | 53.97 | 35.67 | 6.5 |
2.2. Assessment of Barcoding Gap
2.3. “Best Match” and “Best Close Match” Analyses
Subgenus | Barcode Region | N Individuals | BM (%) | BCM (%) | Threshold (%) | |||||
---|---|---|---|---|---|---|---|---|---|---|
Correct | Ambiguous | Incorrect | Correct | Ambiguous | Incorrect | No Match | ||||
Astrophea | ITS1 | 53 | 73.58 | 5.66 | 20.75 | 73.58 | 3.77 | 5.66 | 16.98 | 1.51 |
ITS2 | 53 | 73.58 | 3.77 | 22.64 | 73.58 | 3.77 | 9.43 | 13.20 | 2.97 | |
ITS1+2 | 53 | 73.58 | 3.77 | 22.64 | 73.58 | 3.77 | 5.66 | 16.98 | 1.92 | |
Decaloba | ITS1 | 314 | 63.05 | 4.13 | 32.80 | 61.78 | 3.82 | 23.24 | 11.14 | 3.77 |
ITS2 | 314 | 50.95 | 16.87 | 32.16 | 50.31 | 16.55 | 25.15 | 7.96 | 3.46 | |
ITS1+2 | 314 | 64.64 | 1.27 | 34.07 | 64.01 | 1.27 | 23.88 | 10.82 | 3.43 | |
Deidamioides | ITS1 | 101 | 96.03 | 0 | 4.96 | 95.04 | 0 | 0 | 4.95 | 2.98 |
ITS2 | 101 | 96.03 | 0 | 4.96 | 95.04 | 0 | 0 | 4.95 | 5.41 | |
ITS1+2 | 101 | 96.03 | 0 | 4.96 | 95.04 | 0 | 0 | 4.95 | 3.56 | |
Passiflora | ITS1 | 287 | 81.53 | 1.74 | 16.72 | 78.39 | 1.39 | 5.57 | 14.63 | 1.83 |
ITS2 | 287 | 54.70 | 28.57 | 16.72 | 50.87 | 27.87 | 9.40 | 11.84 | 1.19 | |
ITS1+2 | 287 | 81.18 | 1.74 | 17.07 | 77.00 | 1.39 | 4.52 | 17.07 | 1.28 |
2.4. Tree-Based Methods
Subgenus | Barcode Region | N Individuals | Correct Identifications (%) | ||||
---|---|---|---|---|---|---|---|
NJ | ML | BI | BM | BCM | |||
Astrophea | ITS1 | 53 | 45.28 | 22.64 | 88.68 | 73.58 | 73.58 |
ITS2 | 53 | 35.85 | 13.21 | 50.94 | 73.58 | 73.58 | |
ITS1+2 | 53 | 49.06 | 49.06 | 56.60 | 73.58 | 73.58 | |
Decaloba | ITS1 | 314 | 23.25 | 22.58 | 33.76 | 63.05 | 61.78 |
ITS2 | 314 | 21.34 | 15.29 | 29.30 | 50.95 | 50.31 | |
ITS1+2 | 314 | 31.85 | 33.76 | 38.22 | 64.64 | 64.01 | |
Deidamioides | ITS1 | 101 | 11.88 | 11.88 | 97.03 | 96.03 | 95.04 |
ITS2 | 101 | 29.70 | 2.97 | 28.71 | 96.03 | 95.04 | |
ITS1+2 | 101 | 28.71 | 27.72 | 98.02 | 96.03 | 95.04 | |
Passiflora | ITS1 | 287 | 28.92 | 7.67 | 65.85 | 81.53 | 78.39 |
ITS2 | 287 | 14.29 | 2.44 | 24.04 | 54.70 | 50.87 | |
ITS1+2 | 287 | 33.80 | 33.10 | 68.64 | 81.18 | 77.00 |
2.5. Statistical Analysis
3. Discussion
4. Experimental Section
4.1. Taxon Sampling
4.2. Data Analysis
4.2.1. Genetic Distance-Based Method
4.2.2. DNA Sequence Similarity-Based Method
4.2.3. Tree-Based Method
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Giudicelli, G.C.; Mäder, G.; Brandão de Freitas, L. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae). Int. J. Mol. Sci. 2015, 16, 7289-7303. https://doi.org/10.3390/ijms16047289
Giudicelli GC, Mäder G, Brandão de Freitas L. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae). International Journal of Molecular Sciences. 2015; 16(4):7289-7303. https://doi.org/10.3390/ijms16047289
Chicago/Turabian StyleGiudicelli, Giovanna Câmara, Geraldo Mäder, and Loreta Brandão de Freitas. 2015. "Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)" International Journal of Molecular Sciences 16, no. 4: 7289-7303. https://doi.org/10.3390/ijms16047289