Browsing by Autor "Mark Nesbitt"

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A highly contiguous, scaffold-level nuclear genome assembly for the Fever tree ( Cinchona pubescens Vahl) as a novel resource for research in the Rubiaceae
(2022) 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
Abstract Background The Andean Fever tree ( Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids, which have been vital to treating malaria for centuries. C. pubescens Vahl, in particular, has been an essential source of income for several countries within its native range in north-western South America. However, an absence of available genomic resources is essential for placing the Cinchona species within the tree of life and setting the foundation for exploring the evolution and biosynthesis of quinine alkaloids. Findings We address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens . Using a combination of ∼120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION 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). 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. 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 study provides the first genomic resource for C. pubescens , thus opening new research avenues, including the provision of crucial genetic resources for analysis of alkaloid biosynthesis in the Fever tree.
A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research
(2022) 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
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.
Historical chemical annotations of Cinchona bark collections are comparable to results from current day high-pressure liquid chromatography technologies
(Elsevier BV, 2019) Nataly Allasi Canales; Tobias Gress; Claus Cornett; Kim Walker; Felix Driver; Alexandre Antonelli; Carla Maldonado; Mark Nesbitt; Christopher J. Barnes; Nina Rønsted