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Detection of Snps in Merremia and Its Related Taxa for Species Identification Using Dna Barcode Markers


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1 Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
     

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Merremiae is one of the least defined tribes in the family Convolvulaceae. It contains number of species which are basically herbs and shrubs. Species identification is a tedious work in the tribe using morphological characters as these traits are often influenced by environmental factors. In the present piece of work, we have analysed five taxa (Merremia umbellata, Merremia vitifolia, Merremia tridentata (Pubescens) and Merremia tridentata (Alatipes) along with one species of Ipomoea - Ipomoea calycina) with help of DNA barcode marker. We have used seven DNA barcoding regions from organellar DNA. Clear and reproducible amplifications were obtained in most of the cases but we failed to observe remarkable variation in amplified fragment size. Variations were detected in the DNA sequence associated with matK and rbcL loci. Sequence analysis showed visible difference between the intra and inter specific genetic distance based on K2P model for both the loci. From the sequenced data we found unique SNPs and In/Dels for the different taxa included in the study. Based upon the matK and rbcL SNP variance table, two dendrograms were constructed and authentication of species of Merremia and its relative were carried out. This work will help in authentic identification of the different taxa in the tribe Merremiae.

Keywords

DNA barcode; matK; rbcl; SNPs; K2P.
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  • Austin DF. Convolvulaceae.In Z. L. de Febres and J. A. Steyermark, eds. Vol. 8. Instituto Nacional de Parques, Ediciones Funcación Educatión Ambiental; 1982.

  • Stefanović S, Austin DF, Olmstead RG. Classification of Convolvulaceae: a phylogenetic approach. Syst Bot 2003; 28(4): 791–806.

  • Simoes AR, Culham A, Carine M. Resolving the unresolved tribe: a molecular phylogenetic framework for the Merremieae (Convolvulaceae). Bot J Linn Soc, 2015; 179(3): 374–87.

  • Rivera DE, Ocampo YC, Castro JP, Caro D, Franco LA. Antibacterial activity of Physalis angulata L., Merremia umbellata L., and Cryptostegia grandiflora Roxb. Ex R.Br. - medicinal plants of the Colombian Northern Coast. Orient Pharm Exp Med 2015; 15(1): 95–102.

  • Smith AC. Flora Vitiensis Nova: A New Flora of Fiji (spermatophytes Only). Volume 5, Angiospermae: Dicotyledones, Families 170- 186, Monocotyledones, Family 32, Addenda Et Corrigenda, Index. Pacific Tropical Botanical Garden; 1991.

  • Kamalutheen M, Gopalakrishnan S, Syed Ismail T. Anti-inflammatory and anti-arthritic activities of Merremia tridentata (L.) Hall. f. E-Journal Chem 2009; 6(4): 943–8.

  • Goli V, Vijay Bhaskar K, Prasad Macharla S, Suvarna Devi P, Ramchander T. Effects of Anti-Inflammatory Activity of Mimosa pudica. Asian J Pharm Res 2011; 1(3): 69–71.

  • Karthik KNS, Kumar KR. Evaluation of Analgesic, Anti-Inflammatory of stem bark ethanolic Extract of Michelia champaca Linn . Asian J Pharm Res 2017; 7(2): 94.

  • Anbarasi A, Vidhya R. Evaluation of In Vitro Anti-Inflammatory Activity of Tephrosia purpurea (Seed) . Asian J Pharm Res 2015; 5(2): 83.

  • Weber JM, Ma TS. Microchemical investigations of medicinal plants. XIII. Separation of the alkaloids in the leaves of Ipomoea violacea using thin layer chromatography. Mikrochim Acta 1976; (2-3 Pt 1): 193–225.

  • Staples GW. Generic relationships of Ipomoea, Merremia and Operculina. 1979.

  • Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc London Ser B Biol Sci 2003; 270(1512): 313–21.

  • Hollingsworth PM, Graham SW, Little DP. Choosing and Using a Plant DNA Barcode. PLoS One 2011; 6(5): e19254–e19254.

  • Jena B, Giri AK, Biswal B, Acharya L, Panda MK. Cultivar identification in Tabernaemontana divaricata (L.) R. Br. ex Roem. and Schult. using universal barcode markers. Gene Reports 2019; 17: 100467.

  • Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987; (RESEARCH).

  • Senthilkumar G, Madhanraj P, Panneerselvam A. Studies on DNA Extraction , Molecular Identification and Genetic Evolution of Trichoderma harzianum. Asian J Res Chem 2011; 4(8): 1225–31.

  • Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33(7): 1870–4.

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools. Nucleic Acids Res 1997; 25(24): 4876–82.

  • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16(2): 111–20.

  • Meyer CP, Paulay G. DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLOS Biol 2005; 3(12): e422–e422.

  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4(4): 406–25.

  • Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci, 2004; 101(30): 11030–5.

  • Rebecca LJ, Kumar SA, Sharmila D, Kowsalya E, Lakshmi RMG. Evaluation of Genetic Diversity among Ocimum sanctum . Res J Pharm Technol, 2019; 12(6): 2889.

  • Sheng T, Lu Y, Yang K, et al. Association Between Single Nucleotide Polymorphisms (SNPs) in the Promoter of Adiponectin Gene, Hypoadiponectinemia, and Diabetes. Res J Sci Technol 2016; 8(1): 34.

  • Al-Koofee DAF, Mobarak SMH. PRIMER1: A network service for tetra-arms PCR primer design based on well-known dbSNP. Res J Pharm Technol 2018; 11(8): 3633–7.

  • Singh A, Singh S, Anbarasu A. In silico evaluation of non-synonymous snps in irs-1 gene associated with type ii diabetes mellitus. Res J Pharm Technol 2018; 11(5): 1957–61.

  • Anbarasu K, Jagadeeswari P, Mahendran R. In-silico screening of deleterious NF1 SNPS associated with neurofibromatosis type I. Res J Pharm Technol 2017; 10(9): 3247–50.

  • Anbarasu K, Mahjabeen A, Mahendran R. Insights on impact of missense SNPs of human USH2A associated with usher syndrome II. Res J Pharm Technol 2017; 10(10): 3365–8.


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  • Detection of Snps in Merremia and Its Related Taxa for Species Identification Using Dna Barcode Markers

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Authors

Laxmikanta Acharya
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
Omprakash Mohanta
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
Kamalakanta Satapathy
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
Biswajit Jena
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
Bhagyashree Biswa
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
Alok Kumar Giri
Molecular Biology and Genetic Engineering Lab, Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India

Abstract


Merremiae is one of the least defined tribes in the family Convolvulaceae. It contains number of species which are basically herbs and shrubs. Species identification is a tedious work in the tribe using morphological characters as these traits are often influenced by environmental factors. In the present piece of work, we have analysed five taxa (Merremia umbellata, Merremia vitifolia, Merremia tridentata (Pubescens) and Merremia tridentata (Alatipes) along with one species of Ipomoea - Ipomoea calycina) with help of DNA barcode marker. We have used seven DNA barcoding regions from organellar DNA. Clear and reproducible amplifications were obtained in most of the cases but we failed to observe remarkable variation in amplified fragment size. Variations were detected in the DNA sequence associated with matK and rbcL loci. Sequence analysis showed visible difference between the intra and inter specific genetic distance based on K2P model for both the loci. From the sequenced data we found unique SNPs and In/Dels for the different taxa included in the study. Based upon the matK and rbcL SNP variance table, two dendrograms were constructed and authentication of species of Merremia and its relative were carried out. This work will help in authentic identification of the different taxa in the tribe Merremiae.

Keywords


DNA barcode; matK; rbcl; SNPs; K2P.

References