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Wendt G, Collins JJ. Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596073. [PMID: 38853947 PMCID: PMC11160599 DOI: 10.1101/2024.05.27.596073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Schistosomes are parasitic flatworms responsible for the neglected tropical disease schistosomiasis, causing devastating morbidity and mortality in the developing world. The parasites are protected by a skin-like tegument, and maintenance of this tegument is controlled by a schistosome ortholog of the tumor suppressor TP53. To understand mechanistically how p53-1 controls tegument production, we identified a cyclin dependent kinase inhibitor homolog (cki) that was co-expressed with p53-1. RNA interference of cki resulted in a hyperproliferation phenotype, that, in combination with p53-1 RNA interference yielded abundant tumor-like growths, indicating that cki and p53-1 are bona fide tumor suppressors in Schistosoma mansoni. Interestingly, cki homologs are widely present throughout parasitic flatworms but evidently absent from their free-living ancestors, suggesting this cki homolog came from an ancient horizontal gene transfer event. This in turn implies that the evolution of parasitism in flatworms may have been aided by a highly unusual means of metazoan genetic inheritance.
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Affiliation(s)
- George Wendt
- Department of Pharmacology, University of Texas Southwestern Medical Center
| | - James J Collins
- Department of Pharmacology, University of Texas Southwestern Medical Center
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2
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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4
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Mutuku JM, Cui S, Yoshida S, Shirasu K. Orobanchaceae parasite-host interactions. THE NEW PHYTOLOGIST 2021; 230:46-59. [PMID: 33202061 DOI: 10.1111/nph.17083] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Parasitic plants in the family Orobanchaceae, such as Striga, Orobanche and Phelipanche, often cause significant damage to agricultural crops. The Orobanchaceae family comprises more than 2000 species in about 100 genera, providing an excellent system for studying the molecular basis of parasitism and its evolution. Notably, the establishment of model Orobanchaceae parasites, such as Triphysaria versicolor and Phtheirospermum japonicum, that can infect the model host Arabidopsis, has greatly facilitated transgenic analyses of genes important for parasitism. In addition, recent genomic and transcriptomic analyses of several Orobanchaceae parasites have revealed fascinating molecular insights into the evolution of parasitism and strategies for adaptation in this family. This review highlights recent progress in understanding how Orobanchaceae parasites attack their hosts and how the hosts mount a defense against the threats.
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Affiliation(s)
- J Musembi Mutuku
- The Central and West African Virus Epidemiology (WAVE). Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, BP V34, Abidjan, 01, Côte d'Ivoire
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoko Yoshida
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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5
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Emamalipour M, Seidi K, Zununi Vahed S, Jahanban-Esfahlan A, Jaymand M, Majdi H, Amoozgar Z, Chitkushev LT, Javaheri T, Jahanban-Esfahlan R, Zare P. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression. Front Cell Dev Biol 2020; 8:229. [PMID: 32509768 PMCID: PMC7248198 DOI: 10.3389/fcell.2020.00229] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.
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Affiliation(s)
- Melissa Emamalipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hasan Majdi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - L T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States.,Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland.,Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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6
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Petersen G, Anderson B, Braun HP, Meyer EH, Møller IM. Mitochondria in parasitic plants. Mitochondrion 2020; 52:173-182. [DOI: 10.1016/j.mito.2020.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
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Olofsson JK, Dunning LT, Lundgren MR, Barton HJ, Thompson J, Cuff N, Ariyarathne M, Yakandawala D, Sotelo G, Zeng K, Osborne CP, Nosil P, Christin PA. Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass. Curr Biol 2019; 29:3921-3927.e5. [DOI: 10.1016/j.cub.2019.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/26/2022]
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8
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Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu WB, Kelly EA, Zhang H, Person TN, Altman NS, Axtell MJ, Westwood JH, dePamphilis CW. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. NATURE PLANTS 2019; 5:991-1001. [PMID: 31332314 DOI: 10.1038/s41477-019-0458-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/23/2019] [Indexed: 05/20/2023]
Abstract
Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.
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Affiliation(s)
- Zhenzhen Yang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gunjune Kim
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Future Technology Corporate R&D, Seoul, Republic of Korea
| | - Saima Shahid
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Wen-Bin Yu
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Elizabeth A Kelly
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Huiting Zhang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Thomas Nate Person
- Intercollege Graduate Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Naomi S Altman
- Department of Statistics and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Michael J Axtell
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| | - Claude W dePamphilis
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- Intercollege Graduate Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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Johnson NR, Axtell MJ. Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:76-81. [PMID: 31029811 DOI: 10.1016/j.pbi.2019.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 05/02/2023]
Abstract
Parasitic plants make direct contact with their host's vasculature. In parasitism by Cuscuta, RNA and other macromolecules regularly move between host and parasite. Recently, trans-species microRNA from Cuscuta have been shown to functionally target host genes which have essential roles in host defense. Known pathways for the evolution of microRNAs, and the prevalence of horizontal gene transfer events in the Cuscuta lineage, hint that trans-species microRNAs could originate from captured host genes. It is unknown how the delivery of microRNAs from the parasite to the host takes place. One exciting possibility is through apoplastic export using extracellular vesicles, a process which has recently been shown to transport select small RNAs in plants and fungi. These discoveries represent the initial findings of what may be a widespread mechanism of interactions between species.
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Affiliation(s)
- Nathan R Johnson
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Misra VA, Wafula EK, Wang Y, dePamphilis CW, Timko MP. Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism. BMC PLANT BIOLOGY 2019; 19:196. [PMID: 31088371 PMCID: PMC6515653 DOI: 10.1186/s12870-019-1786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/17/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Root parasitic weeds are a major constraint to crop production worldwide causing significant yearly losses in yield and economic value. These parasites cause their destruction by attaching to their hosts with a unique organ, the haustorium, that allows them to obtain the nutrients (sugars, amino acids, etc.) needed to complete their lifecycle. Parasitic weeds differ in their nutritional requirements and degree of host dependency and the differential expression of sugar transporters is likely to be a critical component in the parasite's post-attachment survival. RESULTS We identified gene families encoding monosaccharide transporters (MSTs), sucrose transporters (SUTs), and SWEETs (Sugars Will Eventually be Exported Transporters) in three root-parasitic weeds differing in host dependency: Triphysaria versicolor (facultative hemiparasite), Phelipanche aegyptiaca (holoparasite), and Striga hermonthica (obligate hemiparasite). The phylogenetic relationship and differential expression profiles of these genes throughout parasite development were examined to uncover differences existing among parasites with different levels of host dependence. Differences in estimated gene numbers are found among the three parasites, and orthologs within the different sugar transporter gene families are found to be either conserved among the parasites in their expression profiles throughout development, or to display parasite-specific differences in developmentally-timed expression. For example, MST genes in the pGLT clade express most highly before host connection in Striga and Triphysaria but not Phelipanche, whereas genes in the MST ERD6-like clade are highly expressed in the post-connection growth stages of Phelipanche but highest in the germination and reproduction stages in Striga. Whether such differences reflect changes resulting from differential host dependence levels is not known. CONCLUSIONS While it is tempting to speculate that differences in estimated gene numbers and expression profiles among members of MST, SUT and SWEET gene families in Phelipanche, Striga and Triphysaria reflect the parasites' levels of host dependence, additional evidence that altered transporter gene expression is causative versus consequential is needed. Our findings identify potential targets for directed manipulation that will allow for a better understanding of the nutrient transport process and perhaps a means for controlling the devastating effects of these parasites on crop productivity.
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Affiliation(s)
- Vikram A. Misra
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
| | - Eric K. Wafula
- Department of Biology, Penn State University, University Park, PA 16802 USA
| | - Yu Wang
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
- Present Address: Center for Quantitative Sciences, Vanderbilt University, 2220 Pierce Avenue, 571 Preston Research Building, Nashville, TN 37232-6848 USA
| | | | - Michael P. Timko
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
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Cusimano N, Renner SS. Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum. AMERICAN JOURNAL OF BOTANY 2019; 106:679-689. [PMID: 31081928 DOI: 10.1002/ajb2.1286] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced. METHODS By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes. RESULTS The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. CONCLUSIONS Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.
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Affiliation(s)
- Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
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12
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Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae). Mol Phylogenet Evol 2019; 132:243-250. [DOI: 10.1016/j.ympev.2018.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 11/23/2022]
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Abstract
A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.
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Kado T, Innan H. Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae. Genome Biol Evol 2018; 10:3196-3210. [PMID: 30407540 PMCID: PMC6294234 DOI: 10.1093/gbe/evy219] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous–synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection.
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Affiliation(s)
- Tomoyuki Kado
- SOKENDAI, Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Hideki Innan
- SOKENDAI, Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
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15
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Vogel A, Schwacke R, Denton AK, Usadel B, Hollmann J, Fischer K, Bolger A, Schmidt MHW, Bolger ME, Gundlach H, Mayer KFX, Weiss-Schneeweiss H, Temsch EM, Krause K. Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris. Nat Commun 2018; 9:2515. [PMID: 29955043 PMCID: PMC6023873 DOI: 10.1038/s41467-018-04344-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 04/23/2018] [Indexed: 11/09/2022] Open
Abstract
A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite's hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.
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Affiliation(s)
- Alexander Vogel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Rainer Schwacke
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, 52428, Germany
| | - Alisandra K Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany.,Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany.,Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, 52428, Germany
| | - Julien Hollmann
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Biologibygget, Framstredet 39, Tromsø, 9037, Norway
| | - Karsten Fischer
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Biologibygget, Framstredet 39, Tromsø, 9037, Norway
| | - Anthony Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Maximilian H-W Schmidt
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, 52428, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München (HMGU), Plant Genome and Systems Biology (PGSB), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München (HMGU), Plant Genome and Systems Biology (PGSB), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Technical University Munich, School of Life Sciences Weihenstephan, Alte Akademie 8, Freising, 85354, Germany
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, Faculty Center Biodiversity, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, Faculty Center Biodiversity, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Biologibygget, Framstredet 39, Tromsø, 9037, Norway.
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16
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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17
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Schneider AC, Moore AJ. Parallel Pleistocene amphitropical disjunctions of a parasitic plant and its host. AMERICAN JOURNAL OF BOTANY 2017; 104:1745-1755. [PMID: 29170246 DOI: 10.3732/ajb.1700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based on the inferred timing of horizontal gene transfer from a papilionoid legume into the common ancestor of Orobanche and Phelipanche. Elevated rates of molecular evolution in the Orobanchaceae have hindered efforts to determine reliable divergence time estimates in the absence of a fossil record. However, using a horizontal gene transfer event as a secondary calibration overcomes this limitation. These chronograms were used to reconstruct the biogeography of Aphyllon, Grindelia, and relatives using a DEC+J model implemented in RevBayes. KEY RESULTS Aphyllon had two amphitropical dispersals from North America to South America, while Grindelia had a single dispersal. The dispersal of the Aphyllon lineage that is parasitic on Grindelia (0.40 Ma) took place somewhat after Grindelia began to diversify in South America (0.93 Ma). Using a secondary calibration based on horizontal gene transfer, we infer more recent divergence dates of holoparasitic Orobancheae than previous studies. CONCLUSIONS Parallel host-parasite amphitropical disjunctions in Grindelia and Aphyllon illustrate one means by which ecological specialization may result in nonindependent patterns of diversity in distantly related lineages. Although Grindelia and Aphyllon both dispersed to South America recently, Grindelia appears to have diversified more extensively following colonization. More broadly, recent Pleistocene glaciations probably have also contributed to patterns of diversity and biogeography of temperate northern hemisphere Orobancheae. We also demonstrate the utility of using horizontal gene transfer events from well-dated clades to calibrate parasite phylogenies in the absence of a fossil record.
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Affiliation(s)
- Adam C Schneider
- Department of Integrative Biology and Jepson Herbarium, 1001 Valley Life Sciences Building, University of California, Berkeley 94720 USA
| | - Abigail J Moore
- Department of Microbiology and Plant Biology and Oklahoma Biological Survey, University of Oklahoma, 770 Van Vleet Oval, Norman, Oklahoma 73019 USA
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18
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Mahelka V, Krak K, Kopecký D, Fehrer J, Šafář J, Bartoš J, Hobza R, Blavet N, Blattner FR. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages. Proc Natl Acad Sci U S A 2017; 114:1726-1731. [PMID: 28137844 PMCID: PMC5320982 DOI: 10.1073/pnas.1613375114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
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MESH Headings
- Cell Nucleus/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Diploidy
- Evolution, Molecular
- Gene Transfer, Horizontal
- Genes, Plant/genetics
- Hordeum/classification
- Hordeum/genetics
- Phylogeny
- Poaceae/classification
- Poaceae/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic;
| | - Karol Krak
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6 16500, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Judith Fehrer
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Roman Hobza
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
- Institute of Biophysics, The Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Nicolas Blavet
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Frank R Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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19
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Yang Z, Zhang Y, Wafula EK, Honaas LA, Ralph PE, Jones S, Clarke CR, Liu S, Su C, Zhang H, Altman NS, Schuster SC, Timko MP, Yoder JI, Westwood JH, dePamphilis CW. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. Proc Natl Acad Sci U S A 2016; 113:E7010-E7019. [PMID: 27791104 PMCID: PMC5111717 DOI: 10.1073/pnas.1608765113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.
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Affiliation(s)
- Zhenzhen Yang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Yeting Zhang
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Loren A Honaas
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Sam Jones
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Christopher R Clarke
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Siming Liu
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Chun Su
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - Huiting Zhang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Stephan C Schuster
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - John I Yoder
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Claude W dePamphilis
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802;
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
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Sun T, Renner SS, Xu Y, Qin Y, Wu J, Sun G. Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. Sci Rep 2016; 6:30192. [PMID: 27452947 PMCID: PMC4958966 DOI: 10.1038/srep30192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich 80638, Germany
| | - Yuxing Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Qin
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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21
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Sun T, Xu Y, Zhang D, Zhuang H, Wu J, Sun G. An acyltransferase gene that putatively functions in anthocyanin modification was horizontally transferred from Fabaceae into the genus Cuscuta. PLANT DIVERSITY 2016; 38:149-155. [PMID: 30159459 PMCID: PMC6112201 DOI: 10.1016/j.pld.2016.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 05/27/2023]
Abstract
Horizontal gene transfer (HGT) refers to the flow of genetic materials to non-offspring, and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability. Anthocyanins are an important group of water-soluble red, purple, or blue secondary metabolites, whose diversity results from modification after the main skeleton biosynthesis. Cuscuta is a stem holoparasitic genus, whose members form direct connection with hosts to withdraw water, nutrients, and macromolecules. Such intimate association is thought to increase the frequency of HGT. By transcriptome screening for foreign genes in Cuscuta australis, we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family, which is likely to be involved in anthocyanin modification, was acquired by C. australis from Fabaceae through HGT. The anthocyanin acyltransferase-like (AT-like) gene was confirmed to be present in the genome assembly of C. australis and the transcriptomes of Cuscuta pentagona. The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yuxing Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Dale Zhang
- College of Life Science, Henan University, 85 Minglun Street, Kaifeng 475001, Henan, China
| | - Huifu Zhuang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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22
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Yoshida S, Cui S, Ichihashi Y, Shirasu K. The Haustorium, a Specialized Invasive Organ in Parasitic Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:643-67. [PMID: 27128469 DOI: 10.1146/annurev-arplant-043015-111702] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.
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Affiliation(s)
- Satoko Yoshida
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Songkui Cui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; , , ,
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23
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Cusimano N, Wicke S. Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae. THE NEW PHYTOLOGIST 2016; 210:680-93. [PMID: 26671255 DOI: 10.1111/nph.13784] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/28/2015] [Indexed: 05/10/2023]
Abstract
Plastid genomes (plastomes) of nonphotosynthetic plants experience extensive gene losses and an acceleration of molecular evolutionary rates. Here, we inferred the mechanisms and timing of reductive genome evolution under relaxed selection in the broomrape family (Orobanchaceae). We analyzed the plastomes of several parasites with a major focus on the genus Orobanche using genome-descriptive and Bayesian phylogenetic-comparative methods. Besides this, we scanned the parasites' other cellular genomes to trace the fate of all genes that were purged from their plastomes. Our analyses indicate that the first functional gene losses occurred within 10 Myr of the transition to obligate parasitism in Orobanchaceae, and that the physical plastome reduction proceeds by small deletions that accumulate over time. Evolutionary rate shifts coincide with the genomic reduction process in broomrapes, suggesting that the shift of selectional constraints away from photosynthesis to other molecular processes alters the plastid rate equilibrium. Most of the photosynthesis-related genes or fragments of genes lost from the plastomes of broomrapes have survived in their nuclear or mitochondrial genomes as the results of multiple intracellular transfers and subsequent fragmentation. Our findings indicate that nonessential DNA is eliminated much faster in the plastomes of nonphotosynthetic parasites than in their other cellular genomes.
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Affiliation(s)
- Natalie Cusimano
- Department of Biology, Ludwig Maximilian University of Munich, Menzinger Street 67, Munich, 80638, Germany
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, Muenster, 48149, Germany
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24
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Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbé Y, Royer C. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC PLANT BIOLOGY 2016; 16:63. [PMID: 26964738 PMCID: PMC4785745 DOI: 10.1186/s12870-016-0745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal peptides produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, among which the model species Medicago truncatula (Mtr), allowed for a genomic analysis of this protein family aimed at i) deciphering the evolutionary history of A1b proteins and their links with A1b-nodulins that are short non-insecticidal disulfide-bonded peptides involved in root nodule signaling and ii) exploring the functional diversity of A1b for novel bioactive molecules. RESULTS Investigating the Mtr genome revealed a remarkable expansion, mainly through tandem duplications, of albumin1 (A1) genes, retaining nearly all of the same canonical structure at both gene and protein levels. Phylogenetic analysis revealed that the ancestral molecule was most probably insecticidal giving rise to, among others, A1b-nodulins. Expression meta-analysis revealed that many A1b coding genes are silent and a wide tissue distribution of the A1 transcripts/peptides within plant organs. Evolutionary rate analyses highlighted branches and sites with positive selection signatures, including two sites shown to be critical for insecticidal activity. Seven peptides were chemically synthesized and folded in vitro, then assayed for their biological activity. Among these, AG41 (aka MtrA1013 isoform, encoded by the orphan TA24778 contig.), showed an unexpectedly high insecticidal activity. The study highlights the unique burst of diversity of A1 peptides within the Medicago genus compared to the other taxa for which full-genomes are available: no A1 member in Lotus, or in red clover to date, while only a few are present in chick pea, soybean or pigeon pea genomes. CONCLUSION The expansion of the A1 family in the Medicago genus is reminiscent of the situation described for another disulfide-rich peptide family, the "Nodule-specific Cysteine-Rich" (NCR), discovered within the same species. The oldest insecticidal A1b toxin was described from the Sophorae, dating the birth of this seed-defense function to more than 58 million years, and making this model of plant/insect toxin/receptor (A1b/insect v-ATPase) one of the oldest known.
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Affiliation(s)
- L. Karaki
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
- />Université de Lyon, F-69000 Lyon, France
| | - P. Da Silva
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Rizk
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - C. Chouabe
- />Université de Lyon, F-69000 Lyon, France
- />UCBL, CarMeN Laboratory, INSERM UMR-1060, Cardioprotection Team, Faculté de Médecine, Univ Lyon-1, Université Claude Bernard Lyon1, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - N. Chantret
- />INRA, UMR1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France
- />Supagro Montpellier, 2 Place Pierre Viala, 34060 Montpellier, France
| | - V. Eyraud
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Gressent
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Sivignon
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - I. Rahioui
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - D. Kahn
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - C. Brochier-Armanet
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Y. Rahbé
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Royer
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
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25
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Abstract
Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.
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26
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Park S, Grewe F, Zhu A, Ruhlman TA, Sabir J, Mower JP, Jansen RK. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. THE NEW PHYTOLOGIST 2015; 208:570-83. [PMID: 25989702 DOI: 10.1111/nph.13467] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.
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Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Andan Zhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Jamal Sabir
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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27
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Davis CC, Xi Z. Horizontal gene transfer in parasitic plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:14-19. [PMID: 26051213 DOI: 10.1016/j.pbi.2015.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
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28
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Kim G, Westwood JH. Macromolecule exchange in Cuscuta-host plant interactions. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:20-5. [PMID: 26051214 DOI: 10.1016/j.pbi.2015.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/01/2015] [Accepted: 05/13/2015] [Indexed: 05/06/2023]
Abstract
Cuscuta species (dodders) are parasitic plants that are able to grow on many different host plants and can be destructive to crops. The connections between Cuscuta and its hosts allow movement of not only water and small nutrients, but also macromolecules including mRNA, proteins and viruses. Recent studies show that RNAs move bidirectionally between hosts and parasites and involve a large number of different genes. Although the function of mobile mRNAs has not been demonstrated in this system, small RNAs are also transmitted and a silencing construct expressed in hosts is able to affect expression of the target gene in the parasite. High throughput sequencing of host-parasite associations has the potential to greatly accelerate understanding of this remarkable interaction.
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Affiliation(s)
- Gunjune Kim
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Latham Hall (0390), Blacksburg, VA 24061, USA
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Latham Hall (0390), Blacksburg, VA 24061, USA.
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29
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Ichihashi Y, Mutuku JM, Yoshida S, Shirasu K. Transcriptomics exposes the uniqueness of parasitic plants. Brief Funct Genomics 2015; 14:275-82. [PMID: 25700082 DOI: 10.1093/bfgp/elv001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Parasitic plants have the ability to obtain nutrients directly from other plants, and several species are serious biological threats to agriculture by parasitizing crops of high economic importance. The uniqueness of parasitic plants is characterized by the presence of a multicellular organ called a haustorium, which facilitates plant-plant interactions, and shutting down or reducing their own photosynthesis. Current technical advances in next-generation sequencing and bioinformatics have allowed us to dissect the molecular mechanisms behind the uniqueness of parasitic plants at the genome-wide level. In this review, we summarize recent key findings mainly in transcriptomics that will give us insights into the future direction of parasitic plant research.
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30
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Yang Z, Wafula EK, Honaas LA, Zhang H, Das M, Fernandez-Aparicio M, Huang K, Bandaranayake PCG, Wu B, Der JP, Clarke CR, Ralph PE, Landherr L, Altman NS, Timko MP, Yoder JI, Westwood JH, dePamphilis CW. Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Mol Biol Evol 2014; 32:767-90. [PMID: 25534030 PMCID: PMC4327159 DOI: 10.1093/molbev/msu343] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative “parasitism genes.” Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.
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Affiliation(s)
- Zhenzhen Yang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Department of Biology, The Pennsylvania State University Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - Loren A Honaas
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Department of Biology, The Pennsylvania State University Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - Huiting Zhang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Department of Biology, The Pennsylvania State University
| | - Malay Das
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University
| | - Monica Fernandez-Aparicio
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University Department of Biology, University of Virginia
| | - Kan Huang
- Department of Biology, University of Virginia
| | | | - Biao Wu
- Department of Plant Sciences, University of California, Davis
| | - Joshua P Der
- Department of Biology, The Pennsylvania State University Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
| | - Christopher R Clarke
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University
| | - Lena Landherr
- Department of Biology, The Pennsylvania State University
| | - Naomi S Altman
- Department of Statistics and Huck Institutes of the Life Sciences, The Pennsylvania State University
| | | | - John I Yoder
- Department of Plant Sciences, University of California, Davis
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University
| | - Claude W dePamphilis
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University Department of Biology, The Pennsylvania State University Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University
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31
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Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH. Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science 2014; 345:808-11. [PMID: 25124438 DOI: 10.1126/science.1253122] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.
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Affiliation(s)
- Gunjune Kim
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Megan L LeBlanc
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric K Wafula
- Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Claude W dePamphilis
- Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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32
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Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GKS, Mathews S, Pryer KM. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A 2014; 111:6672-7. [PMID: 24733898 PMCID: PMC4020063 DOI: 10.1073/pnas.1319929111] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
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Affiliation(s)
- Fay-Wei Li
- Department of Biology, Duke University, Durham, NC 27708
| | - Juan Carlos Villarreal
- Systematic Botany and Mycology, Department of Biology, University of Munich, 80638 Munich, Germany
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Carl J. Rothfels
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Michael Melkonian
- Botany Department, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, NC 27708
| | - Joshua P. Der
- Department of Biology and
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Jarmila Pittermann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | | | | | - Anders Larsson
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Tao Chen
- Fairy Lake Botanical Garden, Shenzhen, Guangdong 518004, China
| | - Stina Weststrand
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Philip Thomas
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | | | | | - Li Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Ying Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | | | - Michael K. Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Douglas E. Soltis
- Florida Museum of Natural History
- Department of Biology, and
- Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | | | - Jane A. Langdale
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1; and
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33
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Zhang D, Qi J, Yue J, Huang J, Sun T, Li S, Wen JF, Hettenhausen C, Wu J, Wang L, Zhuang H, Wu J, Sun G. Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer. BMC PLANT BIOLOGY 2014; 14:19. [PMID: 24411025 PMCID: PMC3893544 DOI: 10.1186/1471-2229-14-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/08/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. RESULTS A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. CONCLUSIONS Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.
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Affiliation(s)
- Dale Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
- College of Life Science, Henan University, 85 Minglun Street, Kaifeng 475001, Henan, China
| | - Jinfeng Qi
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jipei Yue
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jinling Huang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Suoping Li
- College of Life Science, Henan University, 85 Minglun Street, Kaifeng 475001, Henan, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Road, Kunming 650223, Yunnan, China
| | - Christian Hettenhausen
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jinsong Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Lei Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Huifu Zhuang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
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34
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Abstract
The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.
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Affiliation(s)
- Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA; Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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