Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome

Abstract

Leafy spurge (Euphorbia esulaL.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects withE. esulahave helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome forE. esulahas limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome forE. esulawould enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressedE. esulaprotein-coding genes. We also assembled the gene space ofE. esulaby using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate thatE. esulacontains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in ourE. esulaL-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results,E. esulaappears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes ofE. esula.

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

“…ΨpsaI was pseudogenized as TAGCT was inserted ( Figure 3). In the six previously reported Euphorbiaceae plastomes, only psaI exists between accD and ycf4 [25][26][27][28][29][30]. Jatropha curcas is 9 bp longer than other species.…”

“…In the case of Euphorbiaceae, to which Croton belongs, the plastomes of six species have been reported. These species are classified by subfamily as one species of Acalyphoideae (Ricinus communis), four species of Crotonoideae (Hevea brasiliensis, Jatropha curcas and Manihot esculenta) and one species of Euphorbioideae (Euphorbia esula) [25][26][27][28][29][30]. There is no study finding yet for the plastomes of Croton, which is a large genus consisting of 1,250 species.…”

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

“…4). In the six previously reported Euphorbiaceae plastomes, only psaI exists between accD and ycf4 (Asif et al 2010; Daniell et al 2008;Horvath et al 2018;Li et al 2017;Rivarola et al 2011;Tangphatsornruang et al 2011). Jatropha curcas is 9 bp longer than other species.…”

“…Arg., Jatropha curcas L., Manihot esculenta Crantz and Vernicia fordii (Hemsl.) Airy Shaw) (Asif et al 2010; Daniell et al 2008;Li et al 2017;Tangphatsornruang et al 2011) and Euphorbioideae (Euphorbia esula L.) (Horvath et al 2018). There is no published plastome sequences for Croton.…”

Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches

“…The disconnect between comparing individual omics platforms to understand weed genetics, diversity, heterozygosity, and importantly, evolution of herbicide resistance in weeds, especially non-target site resistance, highlights the need to develop an integrated omics platform. As an example of developing blueprints for constructing low-cost genomic assemblies in weed species, Horvath et al (2018) have sequenced gene space and transcriptome assemblies of E. esula that were used to identify promoter sequences, high-quality markers, and repetitive elements. Based on this framework, a reliable sequence for >90% of the expressed E. esula protein-coding genes was made available.…”