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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: [email protected])
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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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References

Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRefGoogle ScholarPubMed
Anderson, JV, Horvath, DP, Chao, WS, Foley, ME, Hernandez, AG, Thimmapuram, J, Liu, L, Gong, GL, Band, M, Kim, R, Mikel, MA (2007) Characterization of an EST database for the perennial weed leafy spurge: an important resource for weed biology research. Weed Sci 55:193–203 CrossRefGoogle Scholar
Bell, GD, Kane, NC, Rieseberg, LH, Adams, KL (2013) RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biol Evol 5:1309–1323 CrossRefGoogle ScholarPubMed
Bhatia, G, Goyal, N, Sharma, S, Upadhyay, SK, Singh, K (2017) Present scenario of long non-coding RNAs in plants. Non Coding RNA 3:16 CrossRefGoogle ScholarPubMed
Bushnell, B (2014) BBMap. https://sourceforge.net/projects/bbmap. Accessed: September 26, 2017Google Scholar
Bushnell, B (2015) BioInfoTools: BBMap. https://github.com/BioInfoTools/BBMap. Accessed: September 26, 2017Google Scholar
CABI (2004) Euphorbia esula (original text by Chao WS and Anderson JV). In: Crop Protection Compendium. 2004 ed. Wallingford, UK: CABIGoogle Scholar
Chao, WS, Doğramaci, M, Horvath, DP, Anderson, JV, Foley, ME (2016) Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge. BMC Plant Biol 16:47 CrossRefGoogle ScholarPubMed
Chao, WS, Doğramaci, M, Horvath, DP, Anderson, JV, Foley, ME (2017) Comparison of phytohormone levels and transcript profiles during seasonal dormancy transitions in underground adventitious buds of leafy spurge. Plant Mol Biol 94:281–302 CrossRefGoogle ScholarPubMed
Chao, WS, Foley, ME, Doğramaci, M, Anderson, JV, Horvath, DP (2011) Alternating temperature breaks dormancy in leafy spurge seeds and impacts signaling networks associated with HY5. Funct Integr Genomics 11:637–649 CrossRefGoogle ScholarPubMed
Chao, WS, Horvath, DP, Anderson, JV, Foley, ME (2005) Potential model weeds to study genomics, ecology, and physiology in the 21st century. Weed Sci 53:929–937 CrossRefGoogle Scholar
Chiara, M, Horner, DS, Spada, A (2013) De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PLoS ONE 8:e80961 CrossRefGoogle ScholarPubMed
Daniell, H, Wurdack, KJ, Kanagaraj, A, Lee, SB, Saski, C, Jansen, RK (2008) The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and multiple losses of the atpF intron in Malpighiales. Theor Appl Genet 116:723–737 CrossRefGoogle ScholarPubMed
Doğramaci, M, Anderson, JV, Chao, WS, Horvath, DP, Hernandez, AG, Mikel, MA, Foley, ME (2017) Foliar glyphosate treatment alters transcript and hormone profiles in crown buds of leafy spurge and induces dwarfed and bushy phenotypes throughout its perennial lifecycle. Plant Genome 10:1–23 CrossRefGoogle ScholarPubMed
Doğramaci, M, Foley, ME, Horvath, DP, Hernandez, AG, Khetani, RS, Fields, CJ, Keating, KM, Mikel, MA, Anderson, JV (2015a) Glyphosate’s impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 16:395 CrossRefGoogle ScholarPubMed
Doğramaci, M, Horvath, DP, Anderson, JV (2015b) Meta-analysis identifies potential molecular markers for endodormancy in crown buds of leafy spurge. Pages 197–219 in Anderson JV ed, Advances in Plant Dormancy. Cham, Switzerland: Springer International CrossRefGoogle Scholar
Doğramaci, M, Horvath, DP, Chao, WS, Foley, ME, Christoffers, MJ, Anderson, JV (2010) Low temperatures impact dormancy status, flowering competence, and transcript profiles in crown buds of leafy spurge. Plant Mol Biol 73:207–226 CrossRefGoogle ScholarPubMed
Dunn, PH (1979) The distribution of leafy spurge (Euphorbia esula) and other weedy Euphorbia spp. in the United States. Weed Sci 27:509–516 CrossRefGoogle Scholar
Freyer, R, Kiefer-Meyer, MC, Kossel, H (1997) Occurrence of plastid RNA editing in all major lineages of land plants. Proc Natl Acad Sci USA 94:6285–6290 CrossRefGoogle ScholarPubMed
Gaines, TA, Lorentz, L, Figge, A, Herrmann, J, Maiwald, F, Ott, MC, Han, H, Busi, R, Yu, Q, Powles, SB, Beffa, R (2014) RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum . Plant J 78:865–876 CrossRefGoogle ScholarPubMed
Gallart, AP, Pulido, AH, de Lagrán, IAM, Sanseverino, W, Cigliano, RA (2016) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res 44(D1): D1161–D1166 Google Scholar
Głowacka, K, Clark, LV, Adhikari, S, Peng, J, Stewart, JR, Nishiwaki, A, Yamada, T, Jørgensen, U, Hodkinson, TR, Gifford, J, Juvik, JA, Sacks, EJ (2015) Genetic variation in Miscanthus x giganteus and the importance of estimating genetic distance thresholds for differentiating clones. GCB Bioenergy 7:386–404 CrossRefGoogle Scholar
Goodstein, DM, Shu, S, Howson, R, Neupane, R, Hayes, RD, Fazo, J, Mitros, T, Dirks, W, Hellsten, U, Putnam, N, Rokhsar, DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40(Database Issue): D1178–D1186 CrossRefGoogle ScholarPubMed
Grabherr, MG, Haas, BJ, Yassour, M, Levin, JZ, Thompson, DA, Amit, I, Adiconis, X, Fan, L, Raychowdhury, R, Zeng, Q, Chen, Z, Mauceli, E, Hacohen, N, Gnirke, A, Rhind, N, di Palma, F, Birren, BW, Nusbaum, C, Lindblad-Toh, K, Friedman, N, Regev, A (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29:644–652 CrossRefGoogle ScholarPubMed
Horvath, DP, Chao, WS, Suttle, JC, Thimmapuram, J, Anderson, JV (2008) Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.). BMC Genomics 9:536 CrossRefGoogle ScholarPubMed
Horvath, DP, Kudrna, D, Talag, J, Anderson, JV, Chao, WS, Wing, R, Foley, ME, Doğramaci, M (2013) BAC library development, and clone characterization for dormancy-responsive DREB4A, DAM, and FT from leafy spurge (Euphorbia esula L.) identifies differential splicing and conserved promoter motifs. Weed Sci 61:303–309 CrossRefGoogle Scholar
Huang, J, Lu, X, Yan, H, Chen, S, Zhang, W, Huang, R, Zheng, Y (2012) Transcriptome characterization and sequencing-based identification of salt-responsive genes in Millettia pinnata, a semi-mangrove plant. DNA Res 19:195–207 CrossRefGoogle ScholarPubMed
Jegga, AG, Sherwood, SP, Carman, JW, Pinski, AT, Phillips, JL, Pestian, JP, Aronow, BJ (2002) Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res 12:1408–1417 CrossRefGoogle ScholarPubMed
Joshi, NA, Fass, JN (2011) Sickle: A Sliding-Window, Adaptive, Quality-based Trimming Tool for FastQ files. Version 1.33. https://github.com/najoshi/sickle. Accessed: August 6, 2017Google Scholar
Kent, WJ (2002) BLAT: The BLAST-like alignment tool. Genome Res 12:656–664 Google ScholarPubMed
Kim, ED, Sung, S (2012) Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci 17:16–21 CrossRefGoogle ScholarPubMed
Lai, Z, Kane, NC, Kozik, A, Hodgins, KA, Dlugosch, KM, Barker, MS, Matvienko, M, Yu, Q, Turner, KG, Pearl, SA, Bell, GD, Zou, Y, Grassa, C, Guggisberg, A, Adams, KL, Anderson, JV, Horvath, DP, Kesseli, RV, Burke, JM, Michelmore, RW, Rieseberg, LH (2012) Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am J Bot 99:209–218 CrossRefGoogle ScholarPubMed
Li, L, Xu, L, Wang, X, Pan, G, Lu, L (2015) De novo characterization of the alligator weed (Alternanthera philoxeroides) transcriptome illuminates gene expression under potassium deprivation. J Genet 94:95–104 CrossRefGoogle ScholarPubMed
Lokko, Y, Anderson, JV, Rudd, S, Raji, A, Horvath, D, Mikel, MA, Kim, R, Liu, L, Hernandez, A, Dixon, AGO (2007) Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Rep 26:1605–1618 CrossRefGoogle Scholar
Lulin, H, Xiao, Y, Pei, S, Wen, T, Shangqin, H (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS ONE 7:e38653 CrossRefGoogle ScholarPubMed
Merchant, N, Lyons, E, Goff, S, Vaughn, M, Ware, D, Micklos, D, Antin, P (2016) The iPlant collaborative: cyberinfrastructure for enabling data to discovery for the life sciences. PLoS Biol 14:e1002342 CrossRefGoogle ScholarPubMed
Murray, MG, Thompson, WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325 CrossRefGoogle ScholarPubMed
Oliver, SL, Lenards, AJ, Barthelson, RA, Merchant, N, McKay, SJ (2013) Using the iPlant collaborative Discovery Environment. Curr Protoc Bioinformatics Unit 1:22 Google Scholar
Palmer, JD, Herbon, LA (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 28:87–97 CrossRefGoogle ScholarPubMed
Parra, G, Bradnam, K, Korf, I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067 CrossRefGoogle ScholarPubMed
Peng, Y, Abercrombie, LLG, Yuan, JS, Riggins, CW, Sammons, RD, Tranel, PJ, Neal Stewart, C (2010) Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes. Pest Manag Sci 66:1053–1062 CrossRefGoogle ScholarPubMed
Peng, Y, Lai, Z, Lane, T, Nageswara-Rao, M, Okada, M, Jasieniuk, M, O’Geen, H, Kim, RW, Sammons, RD, Rieseberg, LH, Neal Stewart, C (2014) De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Plant Physiol 166:1241–1254 CrossRefGoogle ScholarPubMed
Riggins, CW, Peng, YH, Stewart, CN, Tranel, PJ (2010) Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag Sci 66:1042–1052 CrossRefGoogle ScholarPubMed
Rivarola, M, Foster, JT, Chan, AP, Williams, AL, Rice, DW, Liu, X, Melake-Berhan, A, Creasy, HH, Puiu, D, Rosovitz, MJ, Khouri, HM, Beckstrom-Sternberg, SM, Allan, GJ, Keim, P, Ravel, J, Rabinowicz, PD (2011) Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS ONE 6:e21743 CrossRefGoogle ScholarPubMed
Ruby, JG, Bellare, P, DeRisi, JL (2013) PRICE: software for the targeted assembly of components of (meta) genomic sequence data. G3 (Bethesda) 3:865–880 CrossRefGoogle ScholarPubMed
Schliesky, S, Gowik, U, Weber, AP, Brautigam, A (2012) RNA-Seq assembly—are we there yet? Front Plant Sci 3:220 CrossRefGoogle ScholarPubMed
Schulz-Schaeffer, J, Gerhardt, S (1989) Cytotaxonomic analysis of the Euphorbia spp. (leafy spurge) complex. 2. Comparative study of the chromosome morphology. Biologisches Zentralblatt 108:69–76 Google Scholar
Simão, FA, Waterhouse, RM, Ioannidis, P, Kriventseva, EV, Zdobnov, EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212 CrossRefGoogle ScholarPubMed
Smit, AFA, Hubley, R, Green, P (2013–2015) RepeatMasker Open v. 4.0.6. http://www.repeatmasker.org. Accessed: June 17, 2017Google Scholar
Sudheesh, S, Sawbridge, TI, Cogan, NOI, Kennedy, P, Forster, JW, Kaur, S (2015) De novo assembly and characterisation of the field pea transcriptome using RNA-Seq. BMC Genom 16:611 CrossRefGoogle ScholarPubMed
Tagle, D, Koop, B, Goodman, M, Slightom, J, Hess, D, Jones, R (1988) Embryonic ɛ and γ globin genes of a prosimian primate (Galago crassicaudatus): nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol 203:439–455 CrossRefGoogle ScholarPubMed
Wendel, JF, Jackson, SA, Meyers, BC, Wing, RA (2016) Evolution of plant genome architecture. Genome Biol 17:37 CrossRefGoogle ScholarPubMed
Westwood, JH, dePamphilis, CW, Das, M, Fernández-Aparicio, M, Honaas, LA, Timko, MP, Wafula, EK, Wickett, NJ, Yoder, JI (2012) The Parasitic Plant Genome Project: new tools for understanding the biology of Orobanche and Striga . Weed Sci 60:295–306 CrossRefGoogle Scholar
Wyman, SK, Jansen, RK, Boore, JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255 CrossRefGoogle ScholarPubMed
Xue, W, Li, JT, Zhu, YP, Hou, GY, Kong, XF, Kuang, YY, Sun, XW (2013) L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14:604 CrossRefGoogle ScholarPubMed
Zhu, Z, Zhou, C, Yang, J (2015) Molecular phenotypes associated with anomalous stamen development in Alternanthera philoxeroides . Front Plant Sci 6:242 CrossRefGoogle ScholarPubMed
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