The complete genome sequences of 56 Erythroxylum species

Introduction

The coca genus, Erythroxylum, represents a pantropical clade of small trees and shrubs mostly known by the cocaine-alkaloid bearing coca crops (Erythroxylum coca & E. novogranatense). Within the species-rich Erythroxylum genus, about 205 species (75%) occur in the American tropics, with centers of diversity in eastern Brazil, Colombia, and Venezuela. Another center of diversity is Madagascar, with about 33 species (12% of Erythroxylum; (Daly 2004; White 2019).

Many species of Erythroxylum are utilized in traditional medicine, most conspicuously E. monogynum of India as well as the coca crops – which have been cultivated and used for more than 9,000 years (Dillehay et al. 2010; White et al. 2020). A recent review by Lv and colleagues (Lv et al. 2022) reports our state of knowledge on the natural products and bioactivity of the group. The diversity of tropane alkaloids, diterpenes, triterpenes, flavonoids, and derivatives found in Erythroxylum provide a rich source of bioactive compounds for medicinal applications.

Dating back to Darwin (Darwin 1877), Erythroxylum has also served as a case study of the diversity and biology of heterostyly. All species in the group are distylous, with the exception of 11 dioecious species in the Caribbean region (Fuentes Marrero 2018). The genomic basis of distyly in Erythroxylum remains unstudied.

These genome assemblies add to a growing repository of plant biology resources that will assist investigations focused on plant ecology, evolution, and natural products.

Methods

Leaf tissue from individual wild trees was collected for this study. DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp format. The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).

Results

Data Availability

Raw read data and assembled genome sequences are available via Genbank.

Funding

Funding was provided by Iridian Genomes, grant # IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa. Dawson White is supported by the Grainger Bioinformatics Center at the Field Museum and an NSF Postdoctoral Fellowship in Biology, award 2010821.