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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

Published online by Cambridge University Press:  28 February 2018

David P. Horvath ,
Sagar Patel ,
Münevver Doğramaci ,
Wun S. Chao ,
James V. Anderson ,
Michael E. Foley ,
Brian Scheffler ,
Gerard Lazo ,
Kevin Dorn  and
Changhui Yan
...Show all authors
David P. Horvath*
Affiliation:
Research Scientists, USDA-ARS, Red River Valley Agricultural Research Center, Sunflower and Plant Science Research Unit, Fargo, ND, USA
Sagar Patel
Affiliation:
Post-Doctoral Research Associate, Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD, USA
Münevver Doğramaci
Affiliation:
Assistant Professor, University of South Dakota, Sanford School of Medicine, Internal Medicine Department, Sioux Falls, SD, USA
Wun S. Chao
Affiliation:
Research Scientists, USDA-ARS, Red River Valley Agricultural Research Center, Sunflower and Plant Science Research Unit, Fargo, ND, USA
James V. Anderson
Affiliation:
Research Scientists, USDA-ARS, Red River Valley Agricultural Research Center, Sunflower and Plant Science Research Unit, Fargo, ND, USA
Michael E. Foley
Affiliation:
Research Scientists, USDA-ARS, Red River Valley Agricultural Research Center, Sunflower and Plant Science Research Unit, Fargo, ND, USA
Brian Scheffler
Affiliation:
Computational Molecular Biologist, USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
Gerard Lazo
Affiliation:
Research Geneticist, USDA-ARS-WRRC, Crop Improvement and Genetics Research Unit, Albany, CA, USA
Kevin Dorn
Affiliation:
Post-Doctoral Research Associate, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
Changhui Yan
Affiliation:
Associate Professor, Computer Science Department, North Dakota State University, Fargo, ND, USA
Anna Childers
Affiliation:
Research Scientist, Knowledge Services Division, National Agricultural Library, Beltsville, MD, USA
Michel Schatz
Affiliation:
Adjunct Associate Professor, Department of Computer Science and Computational Biology, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY, USA,
Shoshana Marcus
Affiliation:
Professor, Kingsborough Community College, Brooklyn, NY, USA
*
Author for correspondence: David P. Horvath, USDA-ARS, Red River Valley Agricultural Research Center, Sunflower and Plant Science Research Unit, 1605 Albrecht Boulevard, Fargo, ND 58102. (Email: David.horvath@ars.usda.gov)
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Abstract

Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. esula have 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 for E. esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. esula would 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 expressed E. esula protein-coding genes. We also assembled the gene space of E. esula by 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 that E. esula contains 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 our E. esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. esula appears 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 of E. esula.

Keywords

Patrick J. Tranel; University of IllinoisBioinformaticsgenome assemblygenomicstranscriptomics
Type
Weed Biology and Ecology
Information
Weed Science , Volume 66 , Issue 3 , May 2018 , pp. 355 - 367
Copyright
© Weed Science Society of America, 2018 

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