Chloroplast Genome of Lithocarpus Dealbatus: Identification of Hotspots for Sequence Variability and Phylogeny Analysis in Quercoideae, a Sub-family of Fagaceae

BackgroundThere has been phylogenetic ambiguity and species delimitation problem in Lithocarpus genus and the sub-family Quercoideae (Family: Fagaceae). Lithocarpus dealbatus is the dominant genus among the Quercoideae in India. Although several studies have been conducted on regeneration, ecological and economic significance of the species, limited information is available at genome scale. We sequenced and assembled the complete chloroplast genome of L. dealbatus and compared with other Quercoideae members to understand the sequence variations, rearrangements and its phylogenetic lineage in the Quercoideae.ResultsWe assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. There were 133 genes in the cp-genome, including 86 protein coding genes, 39 transfer RNAs, and eight ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed inter-specific similarities within Lithocarpus genus. DNA diversity analysis identified highly diverged coding and non-coding hotspot regions in the genera Lithocarpus, Quercus, Castanea, and Castanopsis. These hot spots can be used as polymorphic barcodes to resolve the phylogenetic relationship at species level. We discovered five barcodes that could aid in species delimitation across the four genera of Quercoideae. The phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with many Quercus species.ConclusionsOur findings provide insights into the chloroplast genome of L. dealbatus, the mutational hotspot regions and repeat elements. These could be utilized as molecular markers/barcodes for detailed studies in population genetics.