Comparative analysis of Lithocarpus chloroplast genomes reveals candidate DNA barcoding loci

Abstract

Lithocarpus or stone oaks (Fagaceae) are ecologically and economically important trees in tropical and subtropical Asia as animal food sources, valuable timber trees, and natural bioactive components. Nonetheless, it was often challenging to identify Lithocarpus at the species level. Using a short sequence of specific regions in the genome, DNA barcoding offers a fast and cost-effective way to catalogue biodiversity and protect endangered species from illegal trades. However, universal barcodes were reported as not always applicable to all plant species. Thus, specific barcodes have been introduced based on the analysis of whole chloroplast genomes. This study aimed to identify specific barcodes for species-level differentiation within the Lithocarpus genus. Publicly available chloroplast genomes of eight Lithocarpus, three Quercus (Fagaceae) as ingroups and two Corylus (Betulaceae) as outgroups were compared. The number of protein-coding genes ranged between 80 – 87. Of 80 orthogroups identified, fifty-nine groups contained single-copy orthologous genes (SOGs). Only two genes showed high sequence variation: matK and ndhF. We recommend future investigation of these two genes as candidate barcoding loci to identify intraspecific variation at species and population levels. These barcodes will accelerate species identification of Lithocarpus from fresh, herbaria or degraded samples.