Building a novel nuclear-organelle genomic framework for the fever tree (Cinchona pubescens Vahl) through short and long-read DNA data assemblies

Background The Andean fever tree ( Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids which have been key to treating malaria for centuries. In particular, C. pubescens Vahl has been an important source of income for several countries in its native range in north-western South America. However, the genomic resources required to place Cinchona species in the tree of life and to explore the evolution and biosynthesis of alkaloids are meagre. Findings Using a combination of ~120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short read Illumina data, we address this gap by providing the first highly contiguous nuclear and organelle genome assemblies and their corresponding annotations. Our nuclear genome assembly consists of 603 scaffolds comprising a total length of 903 Mb, representing ~85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is highly complete, displaying 83% of the BUSCO gene set, and a small fraction of genes (4.6%) classified as fragmented. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using plastid and nuclear datasets. Conclusions Our study provides the first genomic resource for C. pubescens thus opening new research avenues, including the unravelling of the gene toolkit for alkaloid biosynthesis in the fever tree. ### Competing Interest Statement The authors have declared no competing interest.