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

GigaByte. 2022 Oct 6:2022:gigabyte71. doi: 10.46471/gigabyte.71. eCollection 2022.

Abstract

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. 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% of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo 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 C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.

Grants and funding

NR, AA, CB, and NAC received funding from H2020 MSCA-ITN-ETN Plant.ID, a European Union Horizon 2020 research and innovation programme under grant agreement No 765000. OAPE acknowledges financial support from the Swiss Orchid Foundation and the Lady Sainsbury Fellowship at the Royal Botanic Gardens, Kew. PromethION sequencing (flow cells and consumables) were provided by Oxford Nanopore Technologies. AA and NR acknowledge funding from the SciLifeLab 2015 Biodiversity Program. AA is further funded by the Swedish Research Council and the Royal Botanic Gardens, Kew.