DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Experimental Site
2.2. Plant Sample Preparation and Total Genomic DNA Isolation
2.3. PCR Amplification and Purification
2.4. DNA Sequencing
2.5. Bioinformatics Analysis
2.6. RNA Secondary Structure Predictions
3. Results
3.1. PCR Amplification, Sequencing, and Multiple Sequence Alignment
3.2. Phylogenetic Studies, Replacement Rate Matrices, and DNA Barcoding
3.3. ITS2 Secondary Structure Predictions
4. Discussion
4.1. DNA Barcoding Using rbcL, matK, and ITS2 Genes
4.2. ITS2 Marker and RNA Secondary Structure
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Region | Primers | Sequences (5′ to 3′) | Amplicon Size | Amplification Success Rate |
---|---|---|---|---|
matK | matK XF matK 5R | TAATTTACGATCAATTCATTC GTTCTAGCACAAGAAAGTCG | 1000 bp | 90–95% |
rbcL | rbcLa F rbcLa R | ATGTCACCACAAACAGAGACTAAAGC GTAAAATCAAGTCCACCRCG | 600 bp | 90% |
ITS2 | ITS2 S2F ITS2 S3R | ATGCGATA CTTGGTGTGAATTATAGAAT GACGCTTCTCCAGACTACAAT | 300–400 bp | 80–85% |
Sequences | Base Contents (%) | |||||
---|---|---|---|---|---|---|
A | T | G | C | AT | GC | |
matK | 30.75 | 37.56 | 12.56 | 19.13 | 68.31 | 31.69 |
rbcL | 25.80 | 33.41 | 20.28 | 20.51 | 59.20 | 40.80 |
ITS2 | 19.52 | 11.44 | 34.78 | 34.26 | 30.96 | 69.04 |
Voucher Name | matK and rbcL | ITS2 | Species | |||||
---|---|---|---|---|---|---|---|---|
Percent Identity | E Value | Accession No. (matK) | Accession No. (rbcL) | Percent Identity | E Value | Accession No. (ITS2) | ||
RCMC-1 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
RCMC-2 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
RCMC-5 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.37% | 7 × 10−158 | MK961250.1 | C. esculenta |
RCMC-6 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.37% | 7 × 10−158 | MK961250.1 | C. esculenta |
RCMC-10 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.36% | 2 × 10−157 | MK961250.1 | C. esculenta |
DP-25 | 100% | 0.0 | LT995105.1 | MH270468.1 | 100.00% | 1 × 10−160 | MK961250.1 | C. esculenta |
Duradim | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.04% | 1 × 10−155 | MK961250.1 | C. esculenta |
Jhankri | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.36% | 2 × 10−157 | MK961250.1 | C. esculenta |
MK | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.36% | 2 × 10−157 | MK961250.1 | C. esculenta |
Topi | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.68% | 5 × 10−159 | MK961250.1 | C. esculenta |
Satasankha | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.68% | 5 × 10−159 | MK961250.1 | C. esculenta |
TSL | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
P Chandel | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
R5JH10 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.68% | 5 × 10−159 | MK961250.1 | C. esculenta |
R5MK | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.04% | 1 × 10−155 | MK961250.1 | C. esculenta |
R1B9 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
PCT1 | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.05% | 3 × 10−156 | MK961250.1 | C. esculenta |
BBSL | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.68% | 5 × 10−159 | MK961250.1 | C. esculenta |
TOPI-1kR | 100% | 0.0 | LT995105.1 | MH270468.1 | 99.68% | 5 × 10−159 | MK961250.1 | C. esculenta |
BBSR | 100% | 0.0 | LT995105.1 | MH270468.1 | 100.00% | 1 × 10−160 | MK961250.1 | C. esculenta |
matK | |||||
---|---|---|---|---|---|
matK | From/To | A | T | G | C |
A | - | 12.3839 | 5.8154 | 4.9319 | |
T | 10.2083 | - | 5.8096 | 4.9368 | |
G | 10.2083 | 12.3715 | - | 4.9368 | |
C | 10.1981 | 12.3839 | 5.8154 | - | |
rbcL | |||||
rbcL | From/To | A | T | G | C |
A | - | 9.6984 | 7.2905 | 7.2164 | |
T | 9.1319 | - | 7.2832 | 7.2236 | |
G | 9.1319 | 9.6887 | - | 7.2236 | |
C | 9.1227 | 9.6984 | 7.2905 | - | |
ITS2 | |||||
ITS2 | From/To | A | T | G | C |
A | - | 0.5673 | 1.7239 | 18.0123 | |
T | 1.0720 | - | 45.5929 | 1.7201 | |
G | 1.0720 | 15.0027 | - | 1.7201 | |
C | 11.2258 | 0.5673 | 1.7239 | - |
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Devi, M.P.; Dasgupta, M.; Mohanty, S.; Sharma, S.K.; Hegde, V.; Roy, S.S.; Renadevan, R.; Kumar, K.B.; Patel, H.K.; Sahoo, M.R. DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes 2022, 13, 2294. https://doi.org/10.3390/genes13122294
Devi MP, Dasgupta M, Mohanty S, Sharma SK, Hegde V, Roy SS, Renadevan R, Kumar KB, Patel HK, Sahoo MR. DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes. 2022; 13(12):2294. https://doi.org/10.3390/genes13122294
Chicago/Turabian StyleDevi, Mayengbam Premi, Madhumita Dasgupta, Sansuta Mohanty, Susheel Kumar Sharma, Vivek Hegde, Subhra Saikat Roy, Rennya Renadevan, Kinathi Bipin Kumar, Hitendra Kumar Patel, and Manas Ranjan Sahoo. 2022. "DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India" Genes 13, no. 12: 2294. https://doi.org/10.3390/genes13122294
APA StyleDevi, M. P., Dasgupta, M., Mohanty, S., Sharma, S. K., Hegde, V., Roy, S. S., Renadevan, R., Kumar, K. B., Patel, H. K., & Sahoo, M. R. (2022). DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes, 13(12), 2294. https://doi.org/10.3390/genes13122294