Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

Yoshida, Satoko; Kim, Seungill; Wafula, Eric K.; Tanskanen, Jaakko; Kim, Yong-Min; Honaas, Loren; Yang, Zhenzhen; Spallek, Thomas; Conn, Caitlin E.; Ichihashi, Yasunori; Cheong, Kyeongchae; Cui, Songkui; Der, Joshua P.; Gundlach, Heidrun; Jiao, Yuannian; Hori, Chiaki; Ishida, Juliane K.; Kasahara, Hiroyuki; Kiba, Takatoshi; Kim, Myung-Shin; Koo, Namjin; Laohavisit, Anuphon; Lee, Yong-Hwan; Lumba, Shelley; McCourt, Peter; Mortimer, Jenny C.; Mutuku, J. Musembi; Nomura, Takahito; Sasaki-Sekimoto, Yuko; Seto, Yoshiya; Wang, Yu; Wakatake, Takanori; Sakakibara, Hitoshi; Demura, Taku; Yamaguchi, Shinjiro; Yoneyama, Koichi; Manabe, Ri-ichiroh; Nelson, David C.; Schulman, Alan H.; Timko, Michael P.; dePamphilis, Claude W.; Choi, Doil; Shirasu, Ken

doi:10.1016/j.cub.2019.07.086

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

Journal Article · Sun Sep 01 00:00:00 EDT 2019 · Current Biology

DOI:https://doi.org/10.1016/j.cub.2019.07.086· OSTI ID:1770250

Yoshida, Satoko; Kim, Seungill; Wafula, Eric K.; Tanskanen, Jaakko; Kim, Yong-Min; Honaas, Loren; Yang, Zhenzhen; Spallek, Thomas; Conn, Caitlin E.; Ichihashi, Yasunori; Cheong, Kyeongchae; Cui, Songkui; Der, Joshua P.; Gundlach, Heidrun; Jiao, Yuannian; Hori, Chiaki; Ishida, Juliane K.; Kasahara, Hiroyuki; Kiba, Takatoshi; Kim, Myung-Shin more »

Not Available

View Journal Article

Sponsoring Organization:: USDOE

OSTI ID:: 1770250

Journal Information:: Current Biology, Journal Name: Current Biology Journal Issue: 18 Vol. 29; ISSN 0960-9822

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (62)

Synthesis of (+)-Strigol and (+)-Orobanchol, the Germination Stimulants, and Their Stereoisomers by Employing Lipase-Catalyzed Asymmetric Acetylationas the Key Step Hirayama, Kouichi; Mori, Kenji European Journal of Organic Chemistry, Vol. 1999, Issue 9 https://doi.org/10.1002/(SICI)1099-0690(199909)1999:9<2211::AID-EJOC2211>3.0.CO;2-O	journal	September 1999
The haustorium and the chemistry of host recognition in parasitic angiosperms Chang, Mayland; Lynn, David G. Journal of Chemical Ecology, Vol. 12, Issue 2 https://doi.org/10.1007/BF01020572	journal	February 1986
The ?hyaline body? of the root parasiteAlectra orobanchoides benth. (Scrophulariaceae)?Its anatomy, ultrastructure and histochemistry Visser, J. H.; D�rr, Inge; Kollmann, R. Protoplasma, Vol. 121, Issue 1-2 https://doi.org/10.1007/BF01279762	journal	February 1984
Evolution of Gene Regulatory Networks Controlling Body Plan Development Peter, Isabelle S.; Davidson, Eric H. Cell, Vol. 144, Issue 6 https://doi.org/10.1016/j.cell.2011.02.017	journal	March 2011
Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis Wickett, Norman J.; Honaas, Loren A.; Wafula, Eric K. Current Biology, Vol. 21, Issue 24 https://doi.org/10.1016/j.cub.2011.11.011	journal	December 2011
The evolution of parasitism in plants Westwood, James H.; Yoder, John I.; Timko, Michael P. Trends in Plant Science, Vol. 15, Issue 4 https://doi.org/10.1016/j.tplants.2010.01.004	journal	April 2010
Lateral root development in Arabidopsis: fifty shades of auxin Lavenus, Julien; Goh, Tatsuaki; Roberts, Ianto Trends in Plant Science, Vol. 18, Issue 8 https://doi.org/10.1016/j.tplants.2013.04.006	journal	August 2013
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Ancestral polyploidy in seed plants and angiosperms Jiao, Yuannian; Wickett, Norman J.; Ayyampalayam, Saravanaraj Nature, Vol. 473, Issue 7345 https://doi.org/10.1038/nature09916	journal	April 2011
The auxin influx carrier LAX3 promotes lateral root emergence Swarup, Kamal; Benková, Eva; Swarup, Ranjan Nature Cell Biology, Vol. 10, Issue 8 https://doi.org/10.1038/ncb1754	journal	July 2008
In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples Hejátko, Jan; Blilou, Ikram; Brewer, Philip B. Nature Protocols, Vol. 1, Issue 4 https://doi.org/10.1038/nprot.2006.333	journal	November 2006
Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris Vogel, Alexander; Schwacke, Rainer; Denton, Alisandra K. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04344-z	journal	June 2018
Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis Sun, Guiling; Xu, Yuxing; Liu, Hui Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04721-8	journal	July 2018
Aberrant protein phosphatase 2C leads to abscisic acid insensitivity and high transpiration in parasitic Striga Fujioka, Hijiri; Samejima, Hiroaki; Suzuki, Hideyuki Nature Plants, Vol. 5, Issue 3 https://doi.org/10.1038/s41477-019-0362-7	journal	February 2019
Arabidopsis ALF4 encodes a nuclear‐localized protein required for lateral root formation DiDonato, Raymond J.; Arbuckle, Erin; Buker, Shane The Plant Journal, Vol. 37, Issue 3 https://doi.org/10.1046/j.1365-313X.2003.01964.x	journal	January 2004
Cell-specific nitrogen responses mediate developmental plasticity Gifford, M. L.; Dean, A.; Gutierrez, R. A. Proceedings of the National Academy of Sciences, Vol. 105, Issue 2 https://doi.org/10.1073/pnas.0709559105	journal	January 2008
Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation Yang, Zhenzhen; Zhang, Yeting; Wafula, Eric K. Proceedings of the National Academy of Sciences, Vol. 113, Issue 45 https://doi.org/10.1073/pnas.1608765113	journal	October 2016
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences Mirarab, Siavash; Nguyen, Nam; Guo, Sheng Journal of Computational Biology, Vol. 22, Issue 5 https://doi.org/10.1089/cmb.2014.0156	journal	May 2015
DAGchainer: a tool for mining segmental genome duplications and synteny Haas, B. J.; Delcher, A. L.; Wortman, J. R. Bioinformatics, Vol. 20, Issue 18 https://doi.org/10.1093/bioinformatics/bth397	journal	July 2004
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
Scaffolding pre-assembled contigs using SSPACE Boetzer, Marten; Henkel, Christiaan V.; Jansen, Hans J. Bioinformatics, Vol. 27, Issue 4 https://doi.org/10.1093/bioinformatics/btq683	journal	December 2010
Determining the evolutionary history of gene families Ames, Ryan M.; Money, Daniel; Ghatge, Vikramsinh P. Bioinformatics, Vol. 28, Issue 1 https://doi.org/10.1093/bioinformatics/btr592	journal	October 2011
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
PAML 4: Phylogenetic Analysis by Maximum Likelihood Yang, Z. Molecular Biology and Evolution, Vol. 24, Issue 8 https://doi.org/10.1093/molbev/msm088	journal	April 2007
Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty Yang, Zhenzhen; Wafula, Eric K.; Honaas, Loren A. Molecular Biology and Evolution, Vol. 32, Issue 3 https://doi.org/10.1093/molbev/msu343	journal	December 2014
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data Huerta-Cepas, Jaime; Serra, François; Bork, Peer Molecular Biology and Evolution, Vol. 33, Issue 6 https://doi.org/10.1093/molbev/msw046	journal	February 2016
An efficient algorithm for large-scale detection of protein families Enright, A. J. Nucleic Acids Research, Vol. 30, Issue 7 https://doi.org/10.1093/nar/30.7.1575	journal	April 2002
Fine-grained annotation and classification of de novo predicted LTR retrotransposons Steinbiss, Sascha; Willhoeft, Ute; Gremme, Gordon Nucleic Acids Research, Vol. 37, Issue 21 https://doi.org/10.1093/nar/gkp759	journal	September 2009
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 Llorens, C.; Futami, R.; Covelli, L. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1061	journal	October 2010
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations Campbell, Michael S.; Law, MeiYee; Holt, Carson Plant Physiology, Vol. 164, Issue 2 https://doi.org/10.1104/pp.113.230144	journal	December 2013
Strigolactone Hormones and Their Stereoisomers Signal through Two Related Receptor Proteins to Induce Different Physiological Responses in Arabidopsis Scaffidi, Adrian; Waters, Mark T.; Sun, Yueming K. Plant Physiology, Vol. 165, Issue 3 https://doi.org/10.1104/pp.114.240036	journal	May 2014
Gas Exchange Characteristics of the Sorghum- Striga Host-Parasite Association Press, Malcolm C.; Tuohy, Janet M.; Stewart, George R. Plant Physiology, Vol. 84, Issue 3 https://doi.org/10.1104/pp.84.3.814	journal	July 1987
Auxin-Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins Berckmans, Barbara; Vassileva, Valya; Schmid, Stephan P. C. The Plant Cell, Vol. 23, Issue 10 https://doi.org/10.1105/tpc.111.088377	journal	October 2011
Analyzing Lateral Root Development: How to Move Forward De Smet, Ive; White, Philip J.; Bengough, A. Glyn The Plant Cell, Vol. 24, Issue 1 https://doi.org/10.1105/tpc.111.094292	journal	January 2012
Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family Wicke, Susann; Müller, Kai F.; de Pamphilis, Claude W. The Plant Cell, Vol. 25, Issue 10 https://doi.org/10.1105/tpc.113.113373	journal	October 2013
Multiple layers of incompatibility to the parasitic witchweed, Striga hermonthica Yoshida, Satoko; Shirasu, Ken New Phytologist, Vol. 183, Issue 1 https://doi.org/10.1111/j.1469-8137.2009.02840.x	journal	July 2009
Measurements by dna Renaturation of the Genetic Basis of Parasitic Reduction Searcy, Dennis G.; MacInnis, Austin J. Evolution, Vol. 24, Issue 4 https://doi.org/10.1111/j.1558-5646.1970.tb01814.x	journal	December 1970
The genus Striga : a witch profile: Profile of Striga , the witchweed Spallek, Thomas; Mutuku, Musembi; Shirasu, Ken Molecular Plant Pathology, Vol. 14, Issue 9 https://doi.org/10.1111/mpp.12058	journal	July 2013
Massive Horizontal Gene Transfer in Bdelloid Rotifers Gladyshev, E. A.; Meselson, M.; Arkhipova, I. R. Science, Vol. 320, Issue 5880 https://doi.org/10.1126/science.1156407	journal	May 2008
Receptor-Like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root De Smet, I.; Vassileva, V.; De Rybel, B. Science, Vol. 322, Issue 5901 https://doi.org/10.1126/science.1160158	journal	October 2008
Horizontal Gene Transfer by the Parasitic Plant Striga hermonthica Yoshida, S.; Maruyama, S.; Nozaki, H. Science, Vol. 328, Issue 5982 https://doi.org/10.1126/science.1187145	journal	May 2010
Genomic-scale exchange of mRNA between a parasitic plant and its hosts Kim, G.; LeBlanc, M. L.; Wafula, E. K. Science, Vol. 345, Issue 6198 https://doi.org/10.1126/science.1253122	journal	August 2014
Germination of Witchweed (Striga lutea Lour.): Isolation and Properties of a Potent Stimulant Cook, C. E.; Whichard, L. P.; Turner, B. Science, Vol. 154, Issue 3753 https://doi.org/10.1126/science.154.3753.1189	journal	December 1966
Convergent evolution of strigolactone perception enabled host detection in parasitic plants Conn, C. E.; Bythell-Douglas, R.; Neumann, D. Science, Vol. 349, Issue 6247 https://doi.org/10.1126/science.aab1140	journal	July 2015
Probing strigolactone receptors in Striga hermonthica with fluorescence Tsuchiya, Y.; Yoshimura, M.; Sato, Y. Science, Vol. 349, Issue 6250 https://doi.org/10.1126/science.aab3831	journal	August 2015
Structure-function analysis identifies highly sensitive strigolactone receptors in Striga Toh, S.; Holbrook-Smith, D.; Stogios, P. J. Science, Vol. 350, Issue 6257 https://doi.org/10.1126/science.aac9476	journal	October 2015
Strigolactones, a Novel Carotenoid-Derived Plant Hormone Al-Babili, Salim; Bouwmeester, Harro J. Annual Review of Plant Biology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-arplant-043014-114759	journal	April 2015
Screening synteny blocks in pairwise genome comparisons through integer programming Tang, Haibao; Lyons, Eric; Pedersen, Brent BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-102	journal	April 2011
Ultra-fast sequence clustering from similarity networks with SiLiX Miele, Vincent; Penel, Simon; Duret, Laurent BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-116	journal	April 2011
Automated generation of heuristics for biological sequence comparison Slater, Guy St C.; Birney, Ewan BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-31	journal	February 2005
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons Ellinghaus, David; Kurtz, Stefan; Willhoeft, Ute BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-18	journal	January 2008
Comparison of next generation sequencing technologies for transcriptome characterization Wall, P. Kerr; Leebens-Mack, Jim; Chanderbali, André S. BMC Genomics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2164-10-347	journal	January 2009
ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions Zimmermann, Philip; Bleuler, Stefan; Laule, Oliver BioData Mining, Vol. 7, Issue 1 https://doi.org/10.1186/1756-0381-7-18	journal	August 2014
Versatile and open software for comparing large genomes Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L. Genome Biology, Vol. 5, Issue 2, R12 https://doi.org/10.1186/gb-2004-5-2-r12	journal	January 2004
Gene ontology analysis for RNA-seq: accounting for selection bias Young, Matthew D.; Wakefield, Matthew J.; Smyth, Gordon K. Genome Biology, Vol. 11, Issue 2 https://doi.org/10.1186/gb-2010-11-2-r14	journal	January 2010
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy Emms, David M.; Kelly, Steven Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0721-2	journal	August 2015
Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis Waters, M. T.; Nelson, D. C.; Scaffidi, A. Development, Vol. 139, Issue 7 https://doi.org/10.1242/dev.074567	journal	February 2012
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Agrobacterium rhizogenes-Mediated Transformation of the Parasitic Plant Phtheirospermum japonicum Ishida, Juliane K.; Yoshida, Satoko; Ito, Masaki PLoS ONE, Vol. 6, Issue 10 https://doi.org/10.1371/journal.pone.0025802	journal	October 2011
Carbon Acquisition and Assimilation in Parasitic Plants Press, M. C.; Smith, S.; Stewart, G. R. Functional Ecology, Vol. 5, Issue 2 https://doi.org/10.2307/2389265	journal	January 1991
Unleashing the Genome of Brassica Rapa Tang, Haibao; Lyons, Eric Frontiers in Plant Science, Vol. 3 https://doi.org/10.3389/fpls.2012.00172	journal	January 2012

Similar Records

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Journal Article · Sun Oct 11 20:00:00 EDT 2020 · Nature Communications · OSTI ID:1713294

Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation

Conference · Mon Mar 16 00:00:00 EDT 2015 · OSTI ID:1236442

The genome of Laccaria bicolor provides insights into

Journal Article · Mon Dec 31 23:00:00 EST 2007 · Nature · OSTI ID:965334

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

Citation Formats

References (62)

Similar Records

Related Subjects