PRJNA865558
A Highly Contiguous, Scaffold-level Nuclear Genome Assembly for the Fever Tree (Cinchona pubescens Vahl) as a Novel Resource for Rubiaceae Research
The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America. However, genomic resources are lacking, and these are essential for taxonomic and evolutionary study, as well as to explore quinine alkaloid biosynthesis. Here, we provide the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens, using a combination of Oxford Nanopore PromethION-derived long-read data and short-read Illumina data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp, corresponding to ~825% of the full genome (based on a genome size of 1.1 Gbp/1C). We used a combination of de novo and reference-based transcriptome assemblies to annotate 72,305 coding sequences. Our assembly is moderately complete, comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. We also report the C. pubescens plastome, with a length of ~157 Kbp and 37.74% GC content. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including for the analysis of alkaloid biosynthesis in the fever tree.