DNA barcode developement based on chloroplast and ITS genes for species identification of endangered and threated species of Western Ghats, India

Accurate identification is crucial for conserving species, especially in regions such as the Western Ghats, where trade poses a significant threat to endangered and threatened forest species. Traditional morphology-based identification can be challenging and time-consuming, leading to inaccuracies, especially with similar-looking species or dried specimens. Therefore, DNA barcoding offers a potent solution for precise species identification to address illicit trade and address impactful conservation measures. DNA barcoding is a taxonomic technique that uses standardized short DNA sequences to differentiate and classify species. This approach is especially valuable when morphological characteristics alone are insufficient for accurate species identification. In this study, we focused on the development of a DNA barcoding system for the efficient and accurate identification of threatened and endangered important forest species of Western Ghats Karnataka. To develop the DNA barcoding system, a multilocus approach utilizing sixteen standard DNA barcoding markers was used. A total of 47 threatened and endangered forest species from the Western Ghats were selected for this study. Using a larger number of markers to develop DNA barcodes led to the most precise species identification rates. Moreover, the wide availability of DNA barcode databases allows for quick and accurate species identification. In our study, we observed the highest amplification rates for rbcL1 (40 species), psbtrnH2 (36 species), and PsbA-trnH1 (33 species). DNA amplification varied from 11.76% to 94.11%. Notably, the highest DNA amplification rates were detected for A. wightii (94.11%) and A. hondala (92.34%), both of which belong to the Arecaceae and Passifloraceae families, respectively. Sequencing success rates ranged from 37.5% to 100%. This study will aid in the development of a database of available threatened forest species in western Ghats Karnataka and other regions.