Is There a Key Primer for Amplification of Core Land Plant DNA Barcode Regions ( and )?

Overview

Journal Ecol Evol

Date 2025 Feb 18

PMID 39963510

Authors

Leonardo C J Corvalan

Amanda A de Melo-Ximenes

Larissa R Carvalho

Carlos de M E Silva-Neto

Jose A F Diniz-Filho

Mariana P de C Telles

Rhewter Nunes

Affiliations

Soon will be listed here.

Abstract

The DNA barcode is a technique for molecular identification of species. Two core genes, and , are widely used for land plants. In this technique, the selection of primers is a fundamental step for the success of amplification. Then, we aim to evaluate the primer amplification capability for the DNA barcode regions and . We extracted primer sequences from DNA barcode studies in the Web of Science and used chloroplast genome sequences from NCBI for PCR tests using OpenprimeR. Physicochemical properties of PCR were evaluated using OpenprimeR. Our literature review resulted in 366 and 489 different and primers. These were tested in 8665 sequences, 8463 species from 98 orders. Evaluating only the primer and sequence match, the primers with the highest number of sequences covered were 96.39% and 93.81% forward and reverse for , and 91.56% and 61.62% forward and reverse for . No universal primer for all land plants was found, but two primer pairs could amplify > 99% of the sequences. In contrast to the results obtained for the region, the 10 pairs optimized for the greatest coverage of sequences were not covered by > 85% of the sequences. Therefore, it is advisable to pay attention when selecting primers for the region and the need to develop new primers. Here, we recommend a set of primers to cover the largest number of sequences and orders.

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