Browsing by Autor "Catherine Kidner"

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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.
Plant biogeography of rock outcrops in South American tropical lowlands
(International Biogeography Society, 2025) Rosie Clegg; Luísa Azevedo; Maira T. Martinez-Ugarteche; Danilo M. Neves; Catherine Kidner; D. J. N. Hind; Alexandre Antonelli; Lucy Rowland; R. Toby Pennington
Studies of rock outcrops in tropical South America have increased in recent years, but they have often been restricted to individual countries, single biomes or single disciplines (e.g. through a floristic, functional or genetic lens), limiting their generality. We review the current state of knowledge on the geological and floristic diversity of rock outcrops in tropical South America to identify knowledge gaps and generate testable hypotheses for future research into the biogeography and evolution of their plant communities. We find that the diversity of lowland rock outcrop vegetation is disparately documented and we know less about the evolutionary and biogeographic history of these island-like systems. Based on geological and edaphic factors, we classify South American rock outcrops into four main groups: granite/gneiss, quartzite/metamorphosed sandstone, limestone and ironstone. We hypothesise that these lithologies influence the floristic and evolutionary lineage composition of outcrop floras. However, elevation also plays a role through creating microclimatic conditions and by influencing the degree of insularity from the surrounding vegetation. Our literature review suggests that these lithologies support different floras, but confirming this requires further floristic surveys across the full geological diversity of outcrops. We suggest a research framework to: (i) improve knowledge of outcrop floras and how they relate to floras of surrounding biomes; (ii) investigate the relative roles of niche conservatism and evolution using floristic and phylogenetic approaches; and (iii) assess how outcrop species cope with living in naturally fragmented habitats through analysis of recruitment and gene flow using population genetics. Understanding the biogeography of rock outcrop floras can help provide information for conservation planning and decisions. Rock outcrops are in urgent need of study because they possess a distinctive and highly specialised flora that is threatened by climate and land-use changes. There is a need to increase the number of studies in some Latin American countries (e.g. Bolivia, Paraguay, Guyana, French Guiana and Suriname) and lithologies (e.g. limestone). We suggest that the major determinant of floristic composition on rock outcrops is lithology and outline how this can be tested using community-level floristic data. Inferring the phylogenetic relationships of the species endemic to rock outcrops and establishing the environments where their closest relatives occur will be a powerful approach to address questions of niche evolution and niche conservatism in the historical assembly of outcrop floras. Population genetic approaches focusing on plant species that occur both in outcrop habitats and the surrounding vegetation will elucidate their connectivity and, therefore, how insular and vulnerable these environments are.