Cinchona pubescens Genome sequencing and assembly

Using a combination of ~120 Gb of long sequencing reads derived from the OxfordNanopore PromethION platform and 142 Gb of short read Illumina data, we address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies. 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 moderately 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 additional plastid and nuclear datasets.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