Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Plant Sample Preparation
2.3. Total Genomic DNA Isolation
2.4. PCR Amplification
2.5. DNA Sequencing
2.6. Bioinformatics Analysis
2.7. DNA Barcoding and ITS2 Secondary Structure Predictions
3. Results
3.1. Amplification, Sequencing, Multiple Sequence Alignment, and Species Identification
3.2. Phylogenetic Studies
3.3. DNA Barcoding and ITS2 Secondary Structure Predictions
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sl. No. | Region | Primer Name | Sequences (5′ to 3′) | Amplicon Size |
---|---|---|---|---|
1 | matK | matK XF | TAATTTACGATCAATTCATTC | 1500 bp |
matK 5R | GTTCTAGCACAAGAAAGTCG | |||
2 | Kim matK | 3F_Kim matK | CGTACAGTACTTTTGTGTTTACGAG | 1500–1580 bp |
1R_Kim matK | ACCCAGTCCATCTGGAAATCTTGGTTC | |||
3 | rbcL | rbcLa F | ATGTCACCACAAACAGAGACTAAAGC | 600–800 bp |
rbcLa R | GTAAAATCAAGTCCACCRCG | |||
4 | ITS2 | ITS2 S2F | ATGCGATA CTTGGTGTGAATTATAGAAT | 400–800 bp |
ITS2 S3R | GACGCTTCTCCAGACTACAAT |
Barcode Genes | Voucher Specimen | Scientific Name | Accession Number | E Value | Query Coverage | Percent Identity |
---|---|---|---|---|---|---|
matK | Eryngium_AND | E. vaseyi | OP086070 | 0.0 | 100% | 99.76% |
Eryngium_CHB | E. foetidum | OP086071 | 0.0 | 100% | 99.81% | |
Kim matK | Eryngium_AND | E. foetidum | OP086074 | 0.0 | 98% | 99.74% |
Eryngium_CHB | E. foetidum | OP086075 | 0.0 | 100% | 99.87% | |
rbcL | Eryngium_AND | E. foetidum | OP086072 | 0.0 | 100% | 100% |
Eryngium_CHB | E. foetidum | OP086073 | 0.0 | 100% | 100% | |
ITS2 | Eryngium_AND | E. foetidum | ON797393 | 2 × 10−153 | 100% | 100% |
Eryngium_CHB | E. foetidum | ON797394 | 2 × 10−153 | 100% | 100% |
Voucher Specimen | Eryngium_AND | Eryngium_CHB | ||||||
---|---|---|---|---|---|---|---|---|
Markers | matK | Kim matK | rbcL | ITS2 | matK | Kim matK | rbcL | ITS2 |
Sequence length | 823 | 763 | 493 | 300 | 534 | 780 | 476 | 357 |
Alignment length | 823 | 763 | 492 | 300 | 533 | 773 | 419 | 357 |
Maximum score | 1509 | 1399 | 909 | 555 | 979 | 1424 | 774 | 660 |
GC content (%) | 37.18 | 36.70 | 43.00 | 62.33 | 35.96 | 36.28 | 43.28 | 63.31 |
CDS region | 2 | 1 | 1 | – | 2 | 1 | 1 | – |
Amino acid | 274 | 254 | 164 | – | 177 | 260 | 159 | – |
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Acharya, G.C.; Mohanty, S.; Dasgupta, M.; Sahu, S.; Singh, S.; Koundinya, A.V.V.; Kumari, M.; Naresh, P.; Sahoo, M.R. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes 2022, 13, 1678. https://doi.org/10.3390/genes13091678
Acharya GC, Mohanty S, Dasgupta M, Sahu S, Singh S, Koundinya AVV, Kumari M, Naresh P, Sahoo MR. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes. 2022; 13(9):1678. https://doi.org/10.3390/genes13091678
Chicago/Turabian StyleAcharya, Gobinda Chandra, Sansuta Mohanty, Madhumita Dasgupta, Supriya Sahu, Satyapriya Singh, Ayyagari V. V. Koundinya, Meenu Kumari, Ponnam Naresh, and Manas Ranjan Sahoo. 2022. "Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India" Genes 13, no. 9: 1678. https://doi.org/10.3390/genes13091678