PJB-2023-125
Effectiveness of DNA barcodes (rbcL, matK, ITS2) in identifying genera and species in Cactaceae
Lihua Wei, Flor Cristina Pacheco-Reyes, José Ángel Villarreal-Quintanilla, Valentín Robledo-Torres, Juan Antonio Encina-Domínguez, Edgar Eduardo Lara-Ramírez and Miguel Ángel Pérez-Rodríguez
Abstract
In this study, we acquired 234 barcoding sequences (78 rbcL, 78 matK, 78 ITS2) representing 49 species of 28 genera in the family Cactaceae. Then we evaluated the discriminatory power of three DNA barcode regions (rbcL, matK, and ITS2) in species of the family Cactaceae using three methods, BLAST, genetic distance, and neighbour-joining trees. In BLAST analysis, the matK barcode region had the highest identification rate at the generic and species levels (83.33% and 50%, respectively). With the closest genetic distance method, the barcode combination groups had higher discrimination rates than any individual barcode region, of which the three barcodes’ combination (rbcL + matK + ITS2) obtained the highest identification rate (52.56%). In neighbour-joining analysis, the phylogenetic tree generated with the ITS2 region had the highest discrimination rate (92.31%), and the best barcode combination group was the rbcL + matK (87.18%). An overlap between the intra- and interspecific distances was observed from DNA barcoding gap analysis. Our results showed that the matK region had a better efficiency in identification at the generic and species levels in the family Cactaceae. Additionally, we strongly recommend using the ITS2 as a DNA barcode region in this family due to its high classification ability in constructing phylogenetic treess.
To Cite this article:
Wei, L., F.C. Pacheco-Reyes, J.Á. Villarreal-Quintanilla, V. Robledo-Torres, J.A. Encina-Domínguez, E.E. Lara-Ramírez and M.Á. Pérez-Rodríguez. 2024. Effectiveness of DNA barcodes (rbcL, matK, ITS2) in identifying genera and species in Cactaceae. Pak. J. Bot., 56(5): DOI: http://dx.doi.org/10.30848/PJB2024-5(11)
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