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

Nataly Allasi Canales, Oscar A. Pérez-escobar, Robyn F. Powell, Mats Töpel, Catherine Kidner, Mark Nesbitt, Carla Maldonado, Christopher J. Barnes, Nina Rønsted, Natalia A. S. Przelomska, Ilia J. Leitch, Alexandre Antonelli. Gigabyte, 2022. https://doi.org/10.46471/gigabyte.71

In short - Here we present a comprehensive genome assembly of the fever tree (Cinchona pubescens Vahl), which achieved a high level of contiguity, providing a detailed and organized representation of the genetic information of the fever tree. This genome assembly serves as a valuable resource for Rubiaceae research, enabling a deeper understanding of the evolution, genetics, and medicinal properties of this plant family.

The main subject of our study, a beautiful Cinchona pubescens blooming at the Temperate House at Royal Botanic Gardens, Kew - 2019. Photo: NAC.

Knowledge gap - The Cinchona genus has been of historical and economic importance due to its medicinal use against fever and malaria. However, its DNA sequence datasets for are limited to only 252 available DNA Sanger sequences. Furthermore, there are few nuclear and no reference genomes for any species of the genus. Thus, fundamental and applied questions, such ass evolutionary processes of the fever tree and the alkaloid genetic pathways, remain elusive. Therefore, a reference genome assembly represents a major breakthrough for Cinchona and Rubiaceae research.

Results - We used a combination of ∼120 Gb of long reads derived from the Oxford Nanopore PromethION sequencing platform and 142 Gb of short read Illumina data. Our nuclear genome assembly comprises 603 scaffolds comprising a total length of 904 Mb, and the completeness represents ∼85% of the genome size (1.1 Gb/1C).

Additionally, we annotated 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies from different tissues. Our assembly is moderately complete, displaying 83% of the BUSCO gene set and a small fraction of genes (4.6%) classified as fragmented. Additionally, we report C. pubescens plastome with a length of ∼157 Kb and a GC content of 37.74%. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using additional plastid and nuclear datasets.

Conclusions - Our Cinchona pubescens reference genome provides an essential tool for scientists studying this plant family, enabling them to explore various aspects of its biology. With the genome assembly in hand, researchers can investigate the evolutionary history, genetic diversity, and population structure of the fever tree and related species.

Data - The genome sequence data, and nuclear and plastid assemblies are available at the NBCI repository, under the BioProject numbers PRJNA768351, PRJNA865567 and PRJNA865558.