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

Euphorbia 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. peplus is 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 establish E. peplus as a new model, we generated a 267.2 Mb Hi-C-anchored PacBio HiFi nuclear genome assembly with an BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six organs, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number between E. peplus and E. lathyris is likely due to fragmentation and rearrangement rather than chromosomal duplication followed by diploidization of the duplicated sequence. Moreover, we found that the E. peplus genome 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 for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family.

Genome assembly of the milky mangroveExcoecaria agallocha

“…The longest gene transcripts of gene models of E. agallocha and four other chromosome-level genomes from the Euphorbiaceae family, namely Hevea brasiliensis (GCF_030052815.1; Cheng et al, 2023), Manihot esculenta (GCA_033783085.1; Landi et al, 2023), Ricinus communis (GCF_019578655.1; Lu et al, 2022) and Euphorbia peplus (GCA_028411795.1; Johnson et al, 2023) were extracted for retrieving orthologous gene pairs through reciprocal BLASTp hits (e-value 1e-5) using diamond (v2.0.13) (Buchfink et al, 2021). Macrosynteny was analysed between E. agallocha and the other four genomes using MCScanX (Wang et al, 2012) with default parameters.…”

Transcriptional dissection of petty spurge (Euphorbia peplusL.) reproductive structures supports theEuphorbiacyathium as an inflorescence rather than a complete flower

“…GO terms were assigned to E. peplus genes as specified in Johnson et al 2023 (Johnson et al, 2023); GO terms assigned to each gene are included in Supplementary File 6. In order to find which GO terms were enriched in differentially expressed genes in different organs as compared with cyathophylls, we ran TopGO v.2.46.0 using the “classicCount” option, using Fisher’s test to determine significance(Alexa and Rahnenfuhrer, 2021).…”

“…The Johnson et al Euphorbia peplus genome assembly and annotation was accessed through Zenodo(Johnson et al, 2023): https://zenodo.org/records/8033914 The Wang et al Euphorbia lathyris assembly and annotation was accessed through figshare(Wang et al, 2021): https://figshare.com/articles/dataset/High-quality_genome_assembly_of_the_biodiesel_plant_Euphorbia_lathyris/14909913/1 The Liu et al Hevea brasiliensis (rubber tree) assembly and annotation was accessed through NCBI(Liu et al, 2020): https://www.ncbi.nlm.nih.gov/assembly/GCA_010458925.1/. The Xu et al wild Ricinus communis assembly and annotation was accessed through NCBI (Xu et al, 2021): https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_019578655.1/.…”

“…The Johnson et al Euphorbia peplus genome assembly and annotation was accessed through Zenodo (Johnson et al, 2023) stsets. The Glycine max (soybean) Wm82.a4.v1 assembly and annotation was accessed through Phytozome (Valliyodan et al, 2019): https://phytozomenext.jgi.doe.gov/info/Gmax_Wm82_a4_v1.…”

“…Figure 1 Euphorbia peplus L., commonly known as petty spurge, is an emerging model species for Euphorbia with a publicly available genome assembly (Czechowski et al, 2022;Johnson et al, 2023). In E. peplus, each immature cyathium is enclosed within two bracts, called cyathophylls.…”