Primer and Barcode Gap Identification and DNA Barcode Generation for Species Discrimination in Plants

Deepu Mathew, Primer and barcode gap identification and DNA barcode generation for species discrimination in plants. In: Nazeem, P.A. (Ed.), Bioinformatics and its Applications in Agriculture, Bioinformatics Centre, Kerala Agricultural University, pp. 61-74, 2015

doi: 10.5281/zenodo.836315

12 Pages Posted: 9 Jun 2020

See all articles by Deepu Mathew

Deepu Mathew

Kerala Agricultural University

Date Written: June 10, 2015

Abstract

This chapter is the summary of conducting DNA barcoding experiments by beginners. The main problem for DNA barcoding in plants is the standardization of the loci which have to be used for barcoding. Often the sequences for these loci or PCR primer combinations shall not be available. This paper details how the primer combinations could be designed by beginning with the universal primers for each locus and finally how the combination of loci to be standardized. Once the sequences are arrived the big question is how to identify the barcodes and barcode gaps. To annotate the sequences, MEGA is the commonly used software. Steps in MEGA analysis for gene annotation and phylogenetic analysis are presented. This chapter also details how the multiple sequence alignment and the barcode identification has to be presented.

Keywords: Plant Biotechnology, Plant Molecular Biology, DNA Barcode, Protocol, Molecular Taxonomy, Molecular Systematics, Phylogeny

Suggested Citation

Mathew, Deepu, Primer and Barcode Gap Identification and DNA Barcode Generation for Species Discrimination in Plants (June 10, 2015). Deepu Mathew, Primer and barcode gap identification and DNA barcode generation for species discrimination in plants. In: Nazeem, P.A. (Ed.), Bioinformatics and its Applications in Agriculture, Bioinformatics Centre, Kerala Agricultural University, pp. 61-74, 2015 , doi: 10.5281/zenodo.836315, Available at SSRN: https://ssrn.com/abstract=3580017 or http://dx.doi.org/10.2139/ssrn.3580017

Deepu Mathew (Contact Author)

Kerala Agricultural University ( email )

Vellanikkara
Thrissur
India

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