Chromosome-level genome assembly ofEuphorbia peplus, a model system for plant latex, reveals that relative lack of Ty3 transposons contributed to its small genome size

Abstract

AbstractEuphorbia peplus(petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia.E. peplusis not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establishE. peplusas a new model, we generated a 267.2 Mb HiC-anchored PacBio HiFi nuclear genome assembly with an embryophyta BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six tissues, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable acrossEuphorbiaspecies. Using a comparative analysis of our newly sequencedE. peplusgenome with other Euphorbiaceae genomes, we show that variation inEuphorbiachromosome number is likely due to fragmentation and rearrangement rather than aneuploidy. Moreover, we found that theE. peplusgenome is relatively compact compared to related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created forE. pepluswill help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family.Significance statementEuphorbiais one of the five largest genera in the plant kingdom. Despite an impressive phenotypic and metabolic diversity in this genus, only oneEuphorbiagenome has been sequenced so far, restricting insights intoEuphorbiabiology.Euphorbia peplushas excellent potential as a model species due to its latex production, fast growth rate and production of the anticancer drug ingenol mebutate. Here, we present a chromosome-levelE. peplusgenome assembly and publicly accessible resources to support molecular research for this unique species and the broader genus. We also provide an explanation of one reason the genome is so small, and identify more candidate genes for the anticancer drug and related compounds.