The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species

A 541 Mb draft genome of Pterocarpus santalinus is presented and evidence of whole-genome duplication in the Eocene period with expansion of drought responsive gene families is documented. Pterocarpus santalinus Linn. f., popularly known as Red Sanders, is a deciduous tree, endemic to southern parts of Eastern Ghats in India. The heartwood is highly valued in the international market due to its deep red colour, fragrant heartwood and wavy grained texture. In the present study, a high-quality draft genome of P. santalinus was assembled using short and long reads generated from Illumina and Oxford Nanopore Sequencing platforms, respectively. The haploid genome size was estimated at 541 Mb and the hybrid assembly showed 99.60% genome completeness. A total of 51,713 consensus gene set were predicted with 31,437 annotated genes. The age of the whole-genome duplication event in the species was dated at 30-39 mya with 95% confidence suggesting early genome duplication event during the Eocene period. Concurrently, phylogenomic assessment of seven Papilionoideae members including P. santalinus grouped the species based on the tribal classification and established divergence of the tribe Dalbergieae from tribe Trifolieae at ~ 54.20 mya. A significant expansion of water deprivation/drought responsive gene families documented in the study probably explains the occurrence of the species in dry rocky patches. Additionally, re-sequencing of six diverse genotypes predicted one variant every 27 bases. This report presents the first draft genome in the genus Pterocarpus and the unprecedented genomic information generated is expected to accelerate population divergence studies in the species in relation to its endemic nature, support trait-based breeding programme and aid in development of diagnostic tools for timber forensics.