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Comput Biol Chem. 2017 Dec;71:20-31. doi: 10.1016/j.compbiolchem.2017.09.003. Epub 2017 Sep 12.

Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis.

Author information

1
Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt.
2
Genetic Resources Research Department, Agriculture Research Center, Giza, Egypt.
3
Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt; Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates. Electronic address: kmosa@sharjah.ac.ae.
4
The Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.

Abstract

The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated and sequenced 15 rbcL and six matK fragments, but our analysis of the resultant sequences demonstrated a limited ability of matK and rbcL in distinguishing between Triticum accessions. Therefore, we pursued a bioinformatics approach to determine the most useful loci which may be used as DNA barcodes for the Triticum spp. We obtained the 10 available chloroplast genomes of the 10 Triticum species and sub-species from NCBI, and performed chloroplast genome-wide analysis to find the potential barcode loci. A total of 134 chloroplast genes, gene combinations, intergenic regions and intergenic region combinations were tested using a Tree-based method. We were unable to discriminate between Triticum species by using chloroplast genes, gene combinations and intergenic regions. However, a combination of the intergenic region (trnfM-trnT) with either (trnD-psbM), (petN-trnC), (matK-rps16) or (rbcL-psaI) demonstrated a very high discrimination capacity, suggesting their utilization as DNA barcodes for the Triticum plants. Furthermore, our novel DNA barcodes demonstrated high discrimination capacity for other Poaceae members.

KEYWORDS:

DNA barcode; Genome-wide analysis; Intergenic region; MatK; Triticum; rbcL

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