Meta-Analysis Identifies Potential Molecular Markers for Endodormancy in Crown Buds of Leafy Spurge; a Herbaceous Perennial

Doğramacı, Münevver; Horvath, David P.; Anderson, James V.

doi:10.1007/978-3-319-14451-1_12

Cited by 8 publications

(10 citation statements)

References 90 publications

(136 reference statements)

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“…Even though we had less than 20X coverage, we were able to successfully assemble and annotate the entire chloroplast genome and large portions of the mitochondrial genome. We were also able to create a database of putative promoter sequences that should be useful for defining potential transcription factorbinding sites from transcriptomics studies on drought responses and dormancy transitions previously performed on E. esula (Doğramaci et al 2015b). We also discovered that there are novel RNA-editing processes active in the chloroplasts of E. esula.…”

Section: Resultsmentioning

confidence: 97%

“…Additionally, a robust cDNA microarray was developed containing almost all of those unigenes, along with an additional 4,000 unigenes from a distantly related euphorb (cassava [Manihot esculenta Crantz]). With these tools, E. esula has proven to be a model herbaceous perennial species for studying bud dormancy (Doğramaci et al 2015b;Horvath et al 2008); flowering (Doğramaci et al 2010(Doğramaci et al , 2015b; seed dormancy (Chao et al 2011); and the effects of herbicides on plant physiology, growth, and development (Doğramaci et al 2015a(Doğramaci et al , 2017. Some of these transcriptomics studies on E. esula have included next-generation sequencing technologies such as RNA-seq, which have generated large quantities of sequences from transcribed portions of the genome.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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“…This work helped to identify transcripts encoded by a gene with similarity to DORMANCY ASSOCIATED MADS-BOX, which has since been strongly implicated in dormancy processes of several perennial plant systems (Horvath 2015). Meta-analysis of microarray-based transcriptome data also identified transcripts similar to Arabidopsis COP1, HY5, MAF3-like, RD22, and RVE1 as potential molecular markers for endodormancy in E. esula UABs (Doğramacı et al 2015).…”

Section: Transcriptomics To Investigate Bud Dormancy and Vegetative Gmentioning

confidence: 97%

“…Studies have also been done to determine the impact of growth regulators on dormancy by examining changes in transcriptome profiles of E. esula UABs in response to foliar glyphosate treatment (Doğramacı et al 2014(Doğramacı et al , 2015(Doğramacı et al , 2016. Although glyphosate is widely used as a broad-spectrum herbicide (Duke and Powles 2008), it is also known to have hormetic activity (Belz and Duke 2014;Velini et al 2008).…”

Section: Transcriptomics To Investigate Bud Dormancy and Vegetative Gmentioning

confidence: 99%

“…RNA-Seq identified nearly 13,000 differentially expressed transcripts in UABs in response to foliar glyphosate treatment (Doğramacı et al 2015). Of these transcripts, 6,239 had significant changes ≥ 2-fold in either direction, which included transcripts associated with many processes involving shoot apical meristem maintenance and stem growth.…”

Section: Transcriptomics To Investigate Bud Dormancy and Vegetative Gmentioning

confidence: 99%

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

et al. 2018

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Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.

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Comparison of phytohormone levels and transcript profiles during seasonal dormancy transitions in underground adventitious buds of leafy spurge

et al. 2017

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Leafy spurge (Euphorbia esula L.) is an herbaceous perennial weed that maintains its perennial growth habit through generation of underground adventitious buds (UABs) on the crown and lateral roots. These UABs undergo seasonal phases of dormancy under natural conditions, namely para-, endo-, and ecodormancy in summer, fall, and winter, respectively. These dormancy phases can also be induced in growth chambers by manipulating photoperiod and temperature. In this study, UABs induced into the three phases of dormancy under controlled conditions were used to compare changes in phytohormone and transcriptome profiles. Results indicated that relatively high levels of ABA, the ABA metabolite PA, and IAA were found in paradormant buds. When UABs transitioned from para- to endodormancy, ABA and PA levels decreased, whereas IAA levels were maintained. Additionally, transcript profiles associated with regulation of soluble sugars and ethylene activities were also increased during para- to endodormancy transition, which may play some role in maintaining endodormancy status. When crown buds transitioned from endo- to ecodormancy, the ABA metabolites PA and DPA decreased significantly along with the down-regulation of ABA biosynthesis genes, ABA2 and NCED3. IAA levels were also significantly lower in ecodormant buds than that of endodormant buds. We hypothesize that extended cold treatment may trigger physiological stress in endodormant buds, and that these stress-associated signals induced the endo- to ecodormancy transition and growth competence. The up-regulation of NAD/NADH phosphorylation and dephosphorylation pathway, and MAF3-like and GRFs genes, may be considered as markers of growth competency.

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Meta-Analysis Identifies Potential Molecular Markers for Endodormancy in Crown Buds of Leafy Spurge; a Herbaceous Perennial

Cited by 8 publications

References 90 publications

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

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

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

Comparison of phytohormone levels and transcript profiles during seasonal dormancy transitions in underground adventitious buds of leafy spurge

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