DNA Barcoding and Phylogenetic Placement of the Genus Euphorbia L. (Euphorbiaceae) in Egypt †
Abstract
:1. Introduction
2. Experiments
2.1. Taxon Sampling, DNA Extraction, Amplification and Sequencing
2.2. Sequence Editing, Alignment and Phylogenetic Analyses
2.3. BLAST Analysis
3. Results
4. Discussion
5. Conclusions
Author Contributions
Conflicts of Interest
References
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Region | PCR Amplification and Sequencing Success | No. of Taxa | No. of Outgroups | Alignment Length (bp) | Total Variable Characters | Parsimony-İnformative Characters |
---|---|---|---|---|---|---|
matK | 50% | 42 | 4 | 1117 | 286 | 164 (14.7%) |
rbcL | 71.40% | 98 | 20 | 552 | 124 | 70 (12.7%) |
trnL intron | 45.71% | 78 | 20 | 870 | 400 | 274 (31.5%) |
trnL-F spacer | 77.14% | 89 | 20 | 483 | 238 | 179 (37%) |
ITS | 66.4% | 131 | 20 | 875 | 636 | 486 (55.5%) |
ITS1 | 124 | 19 | 362 | 294 | 250 (69%) | |
ITS2 | 127 | 20 | 301 | 244 | 210 (69.8%) | |
ITS + ETS + rbcL + matK + trnL intron + trnL-F spacer | 147 | 20 | 4370 | 1850 | 1365 (31.2%) |
Monophyletic Species in the ML Trees | BLASTn İdentification Success | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ITS | ITS1 | ITS2 | matK | rbcL | trnL-F spacer | trnL intron | ITS + ETS + matK + rbcL+ trnL intron + trnL-F Spacer | ITS | ITS1 | ITS2 | matK | rbcL | trnL-F Spacer | trnL İntron | |
Genus Euphorbia | 77% | X | X | 100% | X | 83% | 97% | 98% | |||||||
E. paralias | 100% | 93% | 91% | X | 100% | 99% | 79% | 100% * | 100% * | 100% * | 98% * | ||||
E. retusa | X | X | X | 62% | X | 100% * | 100% * | 100% * | X | X | |||||
E. grossheimii (E. isthmia) | 100% | 100% | X | X | X | X | X | X | X | X | |||||
E. obovata (E. prolifera) | X | X | X | 98% | X | X | X | X | X | 100% * | X | X | |||
E. falcata | X | X | X | 93% | 100% | X | X | X | X | X | |||||
E. chamaepeplus | X | X | |||||||||||||
E. peplus | 97% | X | X | 100% | X | 90% | X | X | 98–99% * | 98–99% * | 100% * | X | 100% * | 98–100% * | 100% |
E. dendroides | 100% | 97% | 92% | X | X | 83% | 88% | ||||||||
E. terracina | 100% | 99% | 100% | 98% | 93% | 99% | |||||||||
E. dracunculoides | X | X | X | X | 100% | 100% * | 100% | X | X | X | X | ||||
E. exigua | 99% | 91% | 97% | X | 100% | 99% | 64% | ||||||||
E. mauritanica | X | X | 96% | X | X | 93% | 92% | X | |||||||
E. nubica (E. consobrina) | 97% | 94% | 98% | 100% | |||||||||||
E. helioscopia | X | 77% | X | X | X | 100% | 98% | X | 99% * | 99% * | 99% * | 100% * | 98% | 99% * | 100% * |
E. hierosolymitana | 100% | 100% | 98% | 100% | 99% | 100% | |||||||||
E. pterococca | 100% | 100% | 98% | 100% | 100% | 100% | |||||||||
E. acalyphoides | X | X | |||||||||||||
E. cuneata | 100% | 100% | 100% | X | 96% | 94% * | |||||||||
E. hirta | 99% | 98% | 98% | X | X | 95% | X | 94% | 99% * | 100% * | 100% * | 100% | 99% * | 100% * | |
E. indica | 100% | 100% | 100% | 94% | 98% | 100% | |||||||||
E. hyssopifolia | X | X | X | X | X | X | 97% | 100% | 100% | 99% | |||||
E. serpens | 100% | 96% | 97% | 77% | 63% | 100% | 98% | ||||||||
E. scordifolia | X | X | |||||||||||||
E. lasiocarpa | X | X | X | X | X | X | X | 95% | 96% | 90% | 99% | 100% | 99% | X | |
E. prostrata | X | 100% | X | X | X | 97% | X | X | 100% * | 100% * | 100% * | 100% | 100% | 98% * | 100% * |
E. arabica | X | 84% | X | X | 36% | ||||||||||
E. inaequilatera | 56% | X | X | X | X | ||||||||||
E. granulata var. granulata | X | X | X | X | X | X | X | 96% | 96% | X | X | 100% | X | ||
E. heterophylla | 100% | 100% | 97% | 100% | X | 100% | 100% | 99% | 99% * | 98% * | 100% * | 99% * | 100% | 99% * | 93% * |
E. peplis | 100% | X | X | X | X | X | 97% | X | 100% | X | X | ||||
E. forsskalii | X | X | X | X | X | X |
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El-Banhawy, A.; Uluer, D.A.; Fayed, A.A.; Mohamed, M.; Faried, A. DNA Barcoding and Phylogenetic Placement of the Genus Euphorbia L. (Euphorbiaceae) in Egypt . Biol. Life Sci. Forum 2021, 4, 58. https://doi.org/10.3390/IECPS2020-08620
El-Banhawy A, Uluer DA, Fayed AA, Mohamed M, Faried A. DNA Barcoding and Phylogenetic Placement of the Genus Euphorbia L. (Euphorbiaceae) in Egypt . Biology and Life Sciences Forum. 2021; 4(1):58. https://doi.org/10.3390/IECPS2020-08620
Chicago/Turabian StyleEl-Banhawy, Ahmed, Deniz Aygören Uluer, Abdel Aziz Fayed, Mona Mohamed, and Ahmed Faried. 2021. "DNA Barcoding and Phylogenetic Placement of the Genus Euphorbia L. (Euphorbiaceae) in Egypt " Biology and Life Sciences Forum 4, no. 1: 58. https://doi.org/10.3390/IECPS2020-08620
APA StyleEl-Banhawy, A., Uluer, D. A., Fayed, A. A., Mohamed, M., & Faried, A. (2021). DNA Barcoding and Phylogenetic Placement of the Genus Euphorbia L. (Euphorbiaceae) in Egypt . Biology and Life Sciences Forum, 4(1), 58. https://doi.org/10.3390/IECPS2020-08620