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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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  • 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