A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

Abstract

The Andean fever tree (<i>Cinchona</i> L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. <i>C. pubescens</i> Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82<i>%</i> of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of <i>de novo</i> and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place <i>C. pubescens</i> in the Gentianales order. This first genomic resource for <i>C. pubescens</i> opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.