Supporting data for "A Highly Contiguous, Scaffold-level Nuclear Genome Assembly for the Fever Tree (<i>Cinchona pubescens</i> Vahl) as a Novel Resource for Rubiaceae Research"

The Andean fever tree (<i>Cinchona</i>L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids which have been key to treating malaria for centuries. In particular, <i>C. pubescens</i> Vahl has been an important source of income for several countries in its native range in north-western South America. However, the genomic resources required to place <i>Cinchona</i> species in the tree of life and to explore the evolution and biosynthesis of alkaloids are meagre. <br>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, we address this gap by providing the first highly contiguous nuclear and organelle genome assemblies and their corresponding annotations. Our nuclear genome assembly consists of 603 scaffolds comprising a total length of 903 Mb, representing ~85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of <i>de novo</i> and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is highly complete, displaying 83% of the BUSCO gene set, and a small fraction of genes (4.6%) classified as fragmented. We demonstrate the utility of these novel genomic resources by placing <i>C. pubescens</i> in the Gentianales order using plastid and nuclear datasets. <br>Our study provides the first genomic resource for <i>C. pubescens</i> thus opening new research avenues, including the unravelling of the gene toolkit for alkaloid biosynthesis in the fever tree.

搜集汇总

背景与挑战

背景概述

该数据集为金鸡纳树（Cinchona pubescens）提供了首个高连续性的核基因组和细胞器基因组组装及注释，结合了约120Gb的Oxford Nanopore长读段和142Gb的Illumina短读段数据，组装基因组大小为903Mb，约占估计基因组大小的85%，并注释了72,305个编码序列。该资源通过质体与核数据集成功将C. pubescens定位在龙胆目系统发育中，为研究抗疟药物奎宁的生物合成和茜草科基因组学提供了重要基础。