De novo genome Assembly of Rauvolfia Serpentina and comparative paleodemographic analysis of Apocynaceae plants

Abstract

Rauvolfia serpentina is a perennial subshrub widely distributed across Asia and the Indian subcontinent. Belonging to the medicinally important Apocynaceae family, it is renowned for its ecological importance and ethnobotanical applications, especially through the biosynthesis of therapeutic indole alkaloids. In this study, we present a de novo genome assembly and annotation for R. serpentina. The assembled genome comprises approximately 184,000 scaffolds with a scaffold N50 of 7.18 Kbp and a high BUSCO completeness score of [~]90% encompassing [~]22,000 annotated genes. We analysed the paleodemographic histories of nine additional Apocynaceae species using Pairwise Sequentially Markovian Coalescent (PSMC) modelling to place these findings in a broader evolutionary context. This comparative analysis revealed a consistent signature of a pronounced bottleneck across the family during the Mid-Pleistocene glaciations, with few notable species showing high adaptive resilience marked by early recovery in effective population size (Ne), while some even showed secondary Ne peaks in the warmer interglacial periods. Although marked by complex and fairly distinct demographic trajectories, most species exhibit stabilised Ne near the onset of the Holocene. The availability of this high-quality draft genome assembly provides an important resource to advance functional, ecological, and comparative genomics in R. serpentina as well as aid heterologous production of pharmaceutically important biomolecules at an industrial scale, thereby alleviating the pressure on wild populations.