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Rancurel C, Legrand L, Danchin EGJ. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes (Basel) 2017; 8:E248. [PMID: 28961181 PMCID: PMC5664098 DOI: 10.3390/genes8100248] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.
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Affiliation(s)
- Corinne Rancurel
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
| | - Ludovic Legrand
- LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan Cedex, France.
| | - Etienne G J Danchin
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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53
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Kikuchi T, Eves-van den Akker S, Jones JT. Genome Evolution of Plant-Parasitic Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:333-354. [PMID: 28590877 DOI: 10.1146/annurev-phyto-080516-035434] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.
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Affiliation(s)
- Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan;
| | - Sebastian Eves-van den Akker
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
- Department of Biological Chemistry, The John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
- School of Biology, University of St. Andrews, North Haugh, St. Andrews, KY16 9TZ, United Kingdom
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54
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Lapadula WJ, Marcet PL, Mascotti ML, Sanchez-Puerta MV, Juri Ayub M. Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer. Sci Rep 2017; 7:1863. [PMID: 28500327 PMCID: PMC5431988 DOI: 10.1038/s41598-017-01859-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/05/2017] [Indexed: 12/26/2022] Open
Abstract
Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms.
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Affiliation(s)
- Walter J Lapadula
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
| | - Paula L Marcet
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Atlanta, USA
| | - María L Mascotti
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Argentina
| | - Maximiliano Juri Ayub
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
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Abstract
Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to
parasitize plants is a derived character that appears to have independently emerged
several times in the phylum Nematoda. Morphological convergence to feeding style has been
observed, but whether this is emergent from molecular convergence is less obvious. To
address this, we assess whether genomic signatures can be associated with plant parasitism
by nematodes. In this review, we report genomic features and characteristics that appear
to be common in plant-parasitic nematodes while absent or rare in animal parasites,
predators or free-living species. Candidate horizontal acquisitions of parasitism genes
have systematically been found in all plant-parasitic species investigated at the sequence
level. Presence of peptides that mimic plant hormones also appears to be a trait of
plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes
available to date have revealed a set of apparently species-specific genes on every
occasion. Effector genes, important for parasitism are frequently found among those
species-specific genes, indicating poor overlap. Overall, nematodes appear to have
developed convergent genomic solutions to adapt to plant parasitism.
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Gillet FX, Bournaud C, Antonino de Souza Júnior JD, Grossi-de-Sa MF. Plant-parasitic nematodes: towards understanding molecular players in stress responses. ANNALS OF BOTANY 2017; 119:775-789. [PMID: 28087659 PMCID: PMC5378187 DOI: 10.1093/aob/mcw260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plant-parasitic nematode interactions occur within a vast molecular plant immunity network. Following initial contact with the host plant roots, plant-parasitic nematodes (PPNs) activate basal immune responses. Defence priming involves the release in the apoplast of toxic molecules derived from reactive species or secondary metabolism. In turn, PPNs must overcome the poisonous and stressful environment at the plant-nematode interface. The ability of PPNs to escape this first line of plant immunity is crucial and will determine its virulence. SCOPE Nematodes trigger crucial regulatory cytoprotective mechanisms, including antioxidant and detoxification pathways. Knowledge of the upstream regulatory components that contribute to both of these pathways in PPNs remains elusive. In this review, we discuss how PPNs probably orchestrate cytoprotection to resist plant immune responses, postulating that it may be derived from ancient molecular mechanisms. The review focuses on two transcription factors, DAF-16 and SKN-1 , which are conserved in the animal kingdom and are central regulators of cell homeostasis and immune function. Both regulate the unfolding protein response and the antioxidant and detoxification pathways. DAF-16 and SKN-1 target a broad spectrum of Caenorhabditis elegans genes coding for numerous protein families present in the secretome of PPNs. Moreover, some regulatory elements of DAF-16 and SKN-1 from C. elegans have already been identified as important genes for PPN infection. CONCLUSION DAF-16 and SKN-1 genes may play a pivotal role in PPNs during parasitism. In the context of their hub status and mode of regulation, we suggest alternative strategies for control of PPNs through RNAi approaches.
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Affiliation(s)
- François-Xavier Gillet
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
| | - Caroline Bournaud
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
- Catholic University of Brasilia, Brasília-DF, Brazil
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Ali MA, Azeem F, Li H, Bohlmann H. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1699. [PMID: 29046680 PMCID: PMC5632807 DOI: 10.3389/fpls.2017.01699] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- *Correspondence: Muhammad A. Ali ;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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58
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Abstract
Lateral gene transfer (LGT) is the transmission of genes, sometimes across species barriers, outwith the classic vertical inheritance from parent to offspring. LGT is recognized as an important phenomenon that has shaped the genomes and biology of prokaryotes. Whether LGT in eukaryotes is important and widespread remains controversial. A study in BMC Biology concludes that LGT in eukaryotes is neither continuous nor prevalent and suggests a rule of thumb for judging when apparent LGT may reflect contamination.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0315-9 .
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Affiliation(s)
- Etienne G J Danchin
- Institut Sophia Agrobiotech, INRA, University of Nice Sophia Antipolis, CNRS, 06903, Sophia Antipolis, France.
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59
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Wu GL, Kuo TH, Tsay TT, Tsai IJ, Chen PJ. Glycoside Hydrolase (GH) 45 and 5 Candidate Cellulases in Aphelenchoides besseyi Isolated from Bird's-Nest Fern. PLoS One 2016; 11:e0158663. [PMID: 27391812 PMCID: PMC4938546 DOI: 10.1371/journal.pone.0158663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/20/2016] [Indexed: 11/18/2022] Open
Abstract
Five Aphelenchoides besseyi isolates collected from bird's-nest ferns or rice possess different parasitic capacities in bird's-nest fern. Two different glycoside hydrolase (GH) 45 genes were identified in the fern isolates, and only one was found in the rice isolates. A Abe GH5-1 gene containing an SCP-like family domain was found only in the fern isolates. Abe GH5-1 gene has five introns suggesting a eukaryotic origin. A maximum likelihood phylogeny revealed that Abe GH5-1 is part of the nematode monophyletic group that can be clearly distinguished from those of other eukaryotic and bacterial GH5 sequences with high bootstrap support values. The fern A. besseyi isolates were the first parasitic plant nematode found to possess both GH5 and GH45 genes. Surveying the genome of the five A. besseyi isolates by Southern blotting using an 834 bp probe targeting the GH5 domain suggests the presence of at least two copies in the fern-origin isolates but none in the rice-origin isolates. The in situ hybridization shows that the Abe GH5-1 gene is expressed in the nematode ovary and testis. Our study provides insights into the diversity of GH in isolates of plant parasitic nematodes of different host origins.
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Affiliation(s)
- Guan-Long Wu
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Tzu-Hao Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Tung-Tsuan Tsay
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Isheng J. Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Peichen J. Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
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60
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Wybouw N, Pauchet Y, Heckel DG, Van Leeuwen T. Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory. Genome Biol Evol 2016; 8:1785-801. [PMID: 27307274 PMCID: PMC4943190 DOI: 10.1093/gbe/evw119] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 01/07/2023] Open
Abstract
Within animals, evolutionary transition toward herbivory is severely limited by the hostile characteristics of plants. Arthropods have nonetheless counteracted many nutritional and defensive barriers imposed by plants and are currently considered as the most successful animal herbivores in terrestrial ecosystems. We gather a body of evidence showing that genomes of various plant feeding insects and mites possess genes whose presence can only be explained by horizontal gene transfer (HGT). HGT is the asexual transmission of genetic information between reproductively isolated species. Although HGT is known to have great adaptive significance in prokaryotes, its impact on eukaryotic evolution remains obscure. Here, we show that laterally transferred genes into arthropods underpin many adaptations to phytophagy, including efficient assimilation and detoxification of plant produced metabolites. Horizontally acquired genes and the traits they encode often functionally diversify within arthropod recipients, enabling the colonization of more host plant species and organs. We demonstrate that HGT can drive metazoan evolution by uncovering its prominent role in the adaptations of arthropods to exploit plants.
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Affiliation(s)
- Nicky Wybouw
- Department of Evolutionary Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Thomas Van Leeuwen
- Department of Evolutionary Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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61
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Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EGJ, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JMC, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJA, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol 2016; 17:124. [PMID: 27286965 PMCID: PMC4901422 DOI: 10.1186/s13059-016-0985-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/12/2016] [Indexed: 11/23/2022] Open
Abstract
Background The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0985-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Peter Thorpe
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | | | - Etienne G J Danchin
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Martine Da Rocha
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Corinne Rancurel
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Nancy E Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Amir Szitenberg
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Eric Grenier
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Josselin Montarry
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Benjamin Mimee
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Marc-Olivier Duceppe
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Ian Boyes
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Hazijah B Yusup
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Joël Lafond-Lapalme
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Magali Esquibet
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Michael Sabeh
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Michael Rott
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Anna Finkers-Tomczak
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | | | - Vivian Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Sophie Mantelin
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Peter J A Cock
- Information and Computational Sciences Group, James Hutton Institute, Dundee, UK
| | - Wendy Phillips
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Bernard Henrissat
- CNRS UMR 7257, INRA, USC 1408, Aix-Marseille University, AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK.,School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
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62
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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63
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Jensen L, Grant JR, Laughinghouse HD, Katz LA. Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa. Evolution 2016; 70:1322-33. [DOI: 10.1111/evo.12935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/04/2016] [Accepted: 04/19/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Lindy Jensen
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Current Address: Department of Molecular and Integrative Physiology; University of Michigan; Ann Arbor Michigan 48109
| | - Jessica R. Grant
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
| | | | - Laura A. Katz
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Program in Organismic and Evolutionary Biology; University of Massachusetts; Amherst Massachusetts 01003
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Noon JB, Baum TJ. Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. BMC Evol Biol 2016; 16:74. [PMID: 27068610 PMCID: PMC4828791 DOI: 10.1186/s12862-016-0651-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/05/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. RESULTS Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches. CONCLUSIONS GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.
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Affiliation(s)
- Jason B. Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
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65
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Rehman S, Gupta VK, Goyal AK. Identification and functional analysis of secreted effectors from phytoparasitic nematodes. BMC Microbiol 2016; 16:48. [PMID: 27001199 PMCID: PMC4802876 DOI: 10.1186/s12866-016-0632-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Plant parasitic nematodes develop an intimate and long-term feeding relationship with their host plants. They induce a multi-nucleate feeding site close to the vascular bundle in the roots of their host plant and remain sessile for the rest of their life. Nematode secretions, produced in the oesophageal glands and secreted through a hollow stylet into the host plant cytoplasm, are believed to play key role in pathogenesis. To combat these persistent pathogens, the identity and functional analysis of secreted effectors can serve as a key to devise durable control measures. In this review, we will recapitulate the knowledge over the identification and functional characterization of secreted nematode effector repertoire from phytoparasitic nematodes. RESEARCH Despite considerable efforts, the identity of genes encoding nematode secreted proteins has long been severely hampered because of their microscopic size, long generation time and obligate biotrophic nature. The methodologies such as bioinformatics, protein structure modeling, in situ hybridization microscopy, and protein-protein interaction have been used to identify and to attribute functions to the effectors. In addition, RNA interference (RNAi) has been instrumental to decipher the role of the genes encoding secreted effectors necessary for parasitism and genes attributed to normal development. Recent comparative and functional genomic approaches have accelerated the identification of effectors from phytoparasitic nematodes and offers opportunities to control these pathogens. CONCLUSION Plant parasitic nematodes pose a serious threat to global food security of various economically important crops. There is a wealth of genomic and transcriptomic information available on plant parasitic nematodes and comparative genomics has identified many effectors. Bioengineering crops with dsRNA of phytonematode genes can disrupt the life cycle of parasitic nematodes and therefore holds great promise to develop resistant crops against plant-parasitic nematodes.
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Affiliation(s)
- Sajid Rehman
- />International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat-Instituts-Morocco, P.O.Box 6299, Rabat, Morocco
| | - Vijai K. Gupta
- />National University of Ireland Galway, Galway, Ireland
| | - Aakash K. Goyal
- />International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat-Instituts-Morocco, P.O.Box 6299, Rabat, Morocco
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66
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Danchin EGJ, Guzeeva EA, Mantelin S, Berepiki A, Jones JT. Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose. Mol Biol Evol 2016; 33:1571-9. [PMID: 26915958 DOI: 10.1093/molbev/msw041] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolution of plant-parasitic nematodes (PPN) is unusual in that these organisms have acquired a range of genes from bacteria via horizontal gene transfer (HGT). The proteins encoded by most of these genes are involved in metabolism of various components of the plant cell wall during invasion of the host. Recent genome sequencing projects for PPN have shown that Glycosyl Hydrolase Family 32 (GH32) sequences are present in several PPN species. These sequences are absent from almost all other animals. Here, we show that the GH32 sequences from an economically important cyst nematode species, Globodera pallida are functional invertases, are expressed during feeding and are restricted in expression to the nematode digestive system. These data are consistent with a role in metabolizing host-derived sucrose. In addition, a detailed phylogenetic analysis shows that the GH32 sequences from PPN and those present in some insect species have distinct bacterial origins and do not therefore derive from a gene present in the last common ancestor of ecdysozoan species. HGT has therefore played at least two critical roles in the evolution of PPN, enabling both invasion of the host and feeding on the main translocation carbohydrate of the plant.
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Affiliation(s)
- Etienne G J Danchin
- Institut Sophia Agrobiotech, INRA, Univ. Nice Sophia Antipolis, CNRS, 06903, Sophia Antipolis, France
| | - Elena A Guzeeva
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom Centre of Parasitology of the A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Sophie Mantelin
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
| | - Adokiye Berepiki
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
| | - John T Jones
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom Biology Department, University of St Andrews, St Andrews, Fife, United Kingdom
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Sonah H, Deshmukh RK, Bélanger RR. Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2016; 7:126. [PMID: 26904083 PMCID: PMC4751359 DOI: 10.3389/fpls.2016.00126] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/23/2016] [Indexed: 05/20/2023]
Abstract
Effector proteins are mostly secretory proteins that stimulate plant infection by manipulating the host response. Identifying fungal effector proteins and understanding their function is of great importance in efforts to curb losses to plant diseases. Recent advances in high-throughput sequencing technologies have facilitated the availability of several fungal genomes and 1000s of transcriptomes. As a result, the growing amount of genomic information has provided great opportunities to identify putative effector proteins in different fungal species. There is little consensus over the annotation and functionality of effector proteins, and mostly small secretory proteins are considered as effector proteins, a concept that tends to overestimate the number of proteins involved in a plant-pathogen interaction. With the characterization of Avr genes, criteria for computational prediction of effector proteins are becoming more efficient. There are 100s of tools available for the identification of conserved motifs, signature sequences and structural features in the proteins. Many pipelines and online servers, which combine several tools, are made available to perform genome-wide identification of effector proteins. In this review, available tools and pipelines, their strength and limitations for effective identification of fungal effector proteins are discussed. We also present an exhaustive list of classically secreted proteins along with their key conserved motifs found in 12 common plant pathogens (11 fungi and one oomycete) through an analytical pipeline.
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Affiliation(s)
| | | | - Richard R. Bélanger
- Département de Phytologie, Faculté des Sciences de l’Agriculture et de l’Alimentation, Centre de Recherche en Horticulture, Université Laval, QuébecQC, Canada
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Vieira P, Eves-van den Akker S, Verma R, Wantoch S, Eisenback JD, Kamo K. The Pratylenchus penetrans Transcriptome as a Source for the Development of Alternative Control Strategies: Mining for Putative Genes Involved in Parasitism and Evaluation of in planta RNAi. PLoS One 2015; 10:e0144674. [PMID: 26658731 PMCID: PMC4684371 DOI: 10.1371/journal.pone.0144674] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/20/2015] [Indexed: 11/25/2022] Open
Abstract
The root lesion nematode Pratylenchus penetrans is considered one of the most economically important species within the genus. Host range studies have shown that nearly 400 plant species can be parasitized by this species. To obtain insight into the transcriptome of this migratory plant-parasitic nematode, we used Illumina mRNA sequencing analysis of a mixed population, as well as nematode reads detected in infected soybean roots 3 and 7 days after nematode infection. Over 140 million paired end reads were obtained for this species, and de novo assembly resulted in a total of 23,715 transcripts. Homology searches showed significant hit matches to 58% of the total number of transcripts using different protein and EST databases. In general, the transcriptome of P. penetrans follows common features reported for other root lesion nematode species. We also explored the efficacy of RNAi, delivered from the host, as a strategy to control P. penetrans, by targeted knock-down of selected nematode genes. Different comparisons were performed to identify putative nematode genes with a role in parasitism, resulting in the identification of transcripts with similarities to other nematode parasitism genes. Focusing on the predicted nematode secreted proteins found in this transcriptome, we observed specific members to be up-regulated at the early time points of infection. In the present study, we observed an enrichment of predicted secreted proteins along the early time points of parasitism by this species, with a significant number being pioneer candidate genes. A representative set of genes examined using RT-PCR confirms their expression during the host infection. The expression patterns of the different candidate genes raise the possibility that they might be involved in critical steps of P. penetrans parasitism. This analysis sheds light on the transcriptional changes that accompany plant infection by P. penetrans, and will aid in identifying potential gene targets for selection and use to design effective control strategies against root lesion nematodes.
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Affiliation(s)
- Paulo Vieira
- Dept. of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, United States of America
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture, Beltsville, MD, 20705–2350, United States of America
| | | | - Ruchi Verma
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture, Beltsville, MD, 20705–2350, United States of America
| | - Sarah Wantoch
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture, Beltsville, MD, 20705–2350, United States of America
| | - Jonathan D. Eisenback
- Dept. of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, United States of America
| | - Kathryn Kamo
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture, Beltsville, MD, 20705–2350, United States of America
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Andam CP, Carver SM, Berthrong ST. Horizontal Gene Flow in Managed Ecosystems. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cheryl P. Andam
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115;
| | - Sarah M. Carver
- Central Research, The Kraft Heinz Company, Glenview, Illinois 60025;
| | - Sean T. Berthrong
- Department of Biological Sciences, Butler University, Indianapolis, Indiana 46208;
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Eyres I, Boschetti C, Crisp A, Smith TP, Fontaneto D, Tunnacliffe A, Barraclough TG. Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. BMC Biol 2015; 13:90. [PMID: 26537913 PMCID: PMC4632278 DOI: 10.1186/s12915-015-0202-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/20/2015] [Indexed: 11/26/2022] Open
Abstract
Background Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly. Results Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species. Conclusions Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0202-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Thomas P Smith
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.
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71
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Zheng M, Long H, Zhao Y, Li L, Xu D, Zhang H, Liu F, Deng G, Pan Z, Yu M. RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae) during Incompatible Infection to Aegilops variabilis. PLoS One 2015; 10:e0141095. [PMID: 26517841 PMCID: PMC4627824 DOI: 10.1371/journal.pone.0141095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae). These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investigated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection) juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process, and three of which were significantly gene-enriched. Besides, the protein-protein interaction network analysis revealed 35 node unigenes which may play an important role in the plant-CCN interaction. Moreover, in a comparison of differentially expressed genes between the pre-parasitic juveniles and the early parasitic juveniles, we found that hydrolase activity was up-regulated in pre J2s whereas binding activity was upregulated in infective J2s. RT-qPCR analysis on some selected genes showed detectable expression, indicating possible secretion of the proteins and putative role in infection. This study provided better insights into the incompatible interaction between H. avenae and the host plant Ae. varabilis. Moreover, RNAi targets with potential lethality were screened out and primarily validated, which provide candidates for engineering-based control of cereal cyst nematode in crops breeding.
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Affiliation(s)
- Minghui Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Lin Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Delin Xu
- Zunyi Medical University, Zunyi, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Feng Liu
- Plant Protection College, Shandong Agriculture University, Tai’an, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Noon JB, Hewezi T, Maier TR, Simmons C, Wei JZ, Wu G, Llaca V, Deschamps S, Davis EL, Mitchum MG, Hussey RS, Baum TJ. Eighteen New Candidate Effectors of the Phytonematode Heterodera glycines Produced Specifically in the Secretory Esophageal Gland Cells During Parasitism. PHYTOPATHOLOGY 2015; 105:1362-72. [PMID: 25871857 DOI: 10.1094/phyto-02-15-0049-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, is the number one pathogen of soybean (Glycine max). This nematode infects soybean roots and forms an elaborate feeding site in the vascular cylinder. H. glycines produces an arsenal of effector proteins in the secretory esophageal gland cells. More than 60 H. glycines candidate effectors were identified in previous gland-cell-mining projects. However, it is likely that additional candidate effectors remained unidentified. With the goal of identifying remaining H. glycines candidate effectors, we constructed and sequenced a large gland cell cDNA library resulting in 11,814 expressed sequence tags. After bioinformatic filtering for candidate effectors using a number of criteria, in situ hybridizations were performed in H. glycines whole-mount specimens to identify candidate effectors whose mRNA exclusively accumulated in the esophageal gland cells, which is a hallmark of many nematode effectors. This approach resulted in the identification of 18 new H. glycines esophageal gland-cell-specific candidate effectors. Of these candidate effectors, 11 sequences were pioneers without similarities to known proteins while 7 sequences had similarities to functionally annotated proteins in databases. These putative homologies provided the bases for the development of hypotheses about potential functions in the parasitism process.
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Affiliation(s)
- Jason B Noon
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Tarek Hewezi
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas R Maier
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Carl Simmons
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Jun-Zhi Wei
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Gusui Wu
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Victor Llaca
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Stéphane Deschamps
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Eric L Davis
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Melissa G Mitchum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Richard S Hussey
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
| | - Thomas J Baum
- First, third, and twelfth authors: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; second author: Department of Plant Sciences, University of Tennessee, Knoxville 37996; fourth, fifth, sixth, seventh, and eighth authors: DuPont Pioneer, Johnston, IA 50131; ninth author: Department of Plant Pathology, North Carolina State University, Raleigh 27695; tenth author: Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia 65211; and eleventh author: Department of Plant Pathology, University of Georgia, Athens 30602
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Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis. Genome Biol Evol 2015; 7:2727-46. [PMID: 26362082 PMCID: PMC4607532 DOI: 10.1093/gbe/evv176] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacterial mutualists can modulate the biochemical capacity of animals. Highly coevolved nutritional mutualists do this by synthesizing nutrients missing from the host’s diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries, and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization, genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed that Xiphinematobacter had a small 0.916-Mb genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum, and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest that Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.
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Affiliation(s)
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | | | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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Mitsumasu K, Seto Y, Yoshida S. Apoplastic interactions between plants and plant root intruders. FRONTIERS IN PLANT SCIENCE 2015; 6:617. [PMID: 26322059 PMCID: PMC4536382 DOI: 10.3389/fpls.2015.00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 07/27/2015] [Indexed: 05/06/2023]
Abstract
Numerous pathogenic or parasitic organisms attack plant roots to obtain nutrients, and the apoplast including the plant cell wall is where the plant cell meets such organisms. Root parasitic angiosperms and nematodes are two distinct types of plant root parasites but share some common features in their strategies for breaking into plant roots. Striga and Orobanche are obligate root parasitic angiosperms that cause devastating agricultural problems worldwide. Parasitic plants form an invasion organ called a haustorium, where plant cell wall degrading enzymes (PCWDEs) are highly expressed. Plant-parasitic nematodes are another type of agriculturally important plant root parasite. These nematodes breach the plant cell walls by protruding a sclerotized stylet from which PCWDEs are secreted. Responding to such parasitic invasion, host plants activate their own defense responses against parasites. Endoparasitic nematodes secrete apoplastic effectors to modulate host immune responses and to facilitate the formation of a feeding site. Apoplastic communication between hosts and parasitic plants also contributes to their interaction. Parasitic plant germination stimulants, strigolactones, are recently identified apoplastic signals that are transmitted over long distances from biosynthetic sites to functioning sites. Here, we discuss recent advances in understanding the importance of apoplastic signals and cell walls for plant-parasite interactions.
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Affiliation(s)
- Kanako Mitsumasu
- Graduate School of Science and Technology, Kumamoto University, Chuo-ku, Japan
| | - Yoshiya Seto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Japan
| | - Satoko Yoshida
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Satoko Yoshida, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan,
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75
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Davies KA, Ye W, Kanzaki N, Bartholomaeus F, Zeng Y, Giblin-Davis RM. A review of the taxonomy, phylogeny, distribution and co-evolution of Schistonchus Cobb, 1927 with proposal of Ficophagus n. gen. and Martininema n. gen. (Nematoda: Aphelenchoididae). NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002907] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The purposes of this paper are to clarify the taxonomic status of the fig-pollinating wasp associateSchistonchussensu lato(Nematoda: Aphelenchoididae) and to suggest directions for future research on the systematics, life history and ecology of the group. Molecular phylogenetic analyses suggest thatSchistonchus s.l.is polyphyletic, and the composition of the three major clades is outlined, together with information on nematode morphology, plant host species, associated pollinating wasp species, and distribution. Biological information and collection data is presented forSchistonchus s.l.fromFicussycones (Moracea) in Africa, Australia, Asia and Central America, and its putative phylogeny is discussed based on molecular and morphological evidence. Both wasps and figs are millions of years old and have worldwide distribution in tropical areas,i.e., opportunities forSchistonchus s.l.-like nematodes to have evolved could have occurred more than once. In addition, figs and their pollinating wasps have variable life histories, which could have provided opportunities forSchistonchus s.l.to also develop different life histories. However, these histories occur inside fig sycones and in association with wasps, which has apparently led to evolutionary convergence and extreme morphological conservatism. Diagnostic characters and their states, derived from examination of described species and morphospecies ofSchistonchus s.l.and informed by molecular phylogenetic inferences, are discussed and illustrated.Schistonchus sensu strictois redefined, andFicophagusn. gen. andMartinineman. gen. are proposed.Schistonchus s.s.is morphologically characterised by having the excretory pore opening in the region of, or posterior to, the metacorpus;Ficophagusn. gen. by having the excretory pore opening very near the cephalic region; andMartinineman. gen. by having it opening at the anterior end of the metacorpus. Several species ofSchistonchus s.s.have a labial disc, but there is no evidence of this in eitherFicophagusn. gen. orMartinineman. gen.
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Affiliation(s)
- Kerrie A. Davies
- Centre for Evolutionary Biology and Biodiversity, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA 5064, Australia
| | - Weimin Ye
- Nematode Assay Section, Agronomic Division, North Carolina Department of Agriculture & Consumer Services, 4300 Reedy Creek Road, Raleigh, NC 27607, USA
| | - Natsumi Kanzaki
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Faerlie Bartholomaeus
- Centre for Evolutionary Biology and Biodiversity, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA 5064, Australia
| | - Yongsan Zeng
- Department of Plant Protection, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P.R. China
| | - Robin M. Giblin-Davis
- Fort Lauderdale Research and Education Center, University of Florida, 3205 College Avenue, Davie, FL 33314-7799, USA
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Danchin EGJ. What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals. Mob Genet Elements 2014; 1:269-273. [PMID: 22545237 PMCID: PMC3337135 DOI: 10.4161/mge.18776] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Horizontal gene transfer (HGT), the transmission of a gene from one species to another by means other than direct vertical descent from a common ancestor, has been recognized as an important phenomenon in the evolutionary biology of prokaryotes. In eukaryotes, in contrast, the importance of HGT has long been overlooked and its evolutionary significance has been considered to be mostly negligible. However, a series of genome analyses has now shown that HGT not only do probably occur at a higher frequency than originally thought in eukaryotes but recent examples have also shown that they have been subject to natural selection, thus suggesting a significant role in the evolutionary history of the receiver species. Surprisingly, these examples are not from protists in which integration and fixation of foreign genes intuitively appear relatively straightforward, because there is no clear distinction between the germline and the somatic genome. Instead, these examples are from nematodes, multicellular animals that do have distinct cells and tissues and do possess a separate germline. Hence, the mechanisms of gene transfer appears in this case much more complicated. In this commentary, I will further discuss two recent publications that describe HGT in nematodes, one that highlights the importance of HGT in the emergence of plant parasitism and another one that probably represents the most convincing example of a potential transfer between two different metazoan animals, an insect and a nematode.
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Affiliation(s)
- Etienne G J Danchin
- Plant-Nematode Interaction; INRA; CNRS; Université de Nice-Sophia Antipolis; Sophia Antipolis, France
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77
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Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida. BMC Genomics 2014; 15:923. [PMID: 25342461 PMCID: PMC4213498 DOI: 10.1186/1471-2164-15-923] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/13/2014] [Indexed: 01/07/2023] Open
Abstract
Background The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium. Results The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure. Conclusion This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-923) contains supplementary material, which is available to authorized users.
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78
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Sagy O, Shamir R, Rechavi O. Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria. Front Genet 2014; 5:275. [PMID: 25221566 PMCID: PMC4148067 DOI: 10.3389/fgene.2014.00275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/26/2014] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing requires insertion of random fragments of the sequenced organism’s DNA into a unicellular host, most often Escherichia coli bacteria. This manipulation was found in the past to be analogous to naturally occurring horizontal gene transfer, and moreover has proved valuable to understanding toxicity of foreign genetic elements to E. coli. Sequencing of the Caenorhabditis elegans genome was similarly achieved via DNA transformation into E. coli. However, numerous attempts have proven a significant percentage of the genome unclonable using bacteria, although clonable via yeast. We examined the genomic segments that were not clonable in bacteria but were clonable in yeast, and observed that, in line with previous hypotheses, such sequences are more repetitive on average compared with the entire C. elegans genome. In addition, we found that these gap-sequences encode significantly more for DNA transposons. Surprisingly, we discovered that although the vast majority of the C. elegans genome is clonable in bacteria (77.5%), almost all the thousands of sequences that encode for PIWI-interacting small RNAs, or 21U-RNAs (91.6%) were only clonable in yeast. These results might help understanding why most piRNAs in C. elegans are physically clustered on particular loci on chromosome IV. In worms and in a large number of other organisms, piRNAs serve to distinguish “Self” from “Non-Self” sequences, and thus to protect the integrity of the genome against foreign genetic elements, such as transposons. We discuss the possible implications of these discoveries.
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Affiliation(s)
- Or Sagy
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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79
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Eves-van den Akker S, Lilley CJ, Danchin EGJ, Rancurel C, Cock PJA, Urwin PE, Jones JT. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biol Evol 2014; 6:2181-94. [PMID: 25123114 PMCID: PMC4202313 DOI: 10.1093/gbe/evu171] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2014] [Indexed: 11/14/2022] Open
Abstract
Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, "specific" have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes.
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Affiliation(s)
- Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, United Kingdom Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom
| | | | - Etienne G J Danchin
- Centre National de la Recherche Scientifique, INRA Institut National de la Recherche Agronomique, UMR 1355, Université de Nice-Sophia Antipolis, Sophia-Antipolis, France
| | - Corinne Rancurel
- Centre National de la Recherche Scientifique, INRA Institut National de la Recherche Agronomique, UMR 1355, Université de Nice-Sophia Antipolis, Sophia-Antipolis, France
| | - Peter J A Cock
- Information and Computational Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, United Kingdom
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom
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80
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De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae. PLoS One 2014; 9:e96311. [PMID: 24802510 PMCID: PMC4011697 DOI: 10.1371/journal.pone.0096311] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.
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81
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Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A, Kanzaki N, Jones JT, Kikuchi T. Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi. BMC Evol Biol 2014; 14:69. [PMID: 24690293 PMCID: PMC3997829 DOI: 10.1186/1471-2148-14-69] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/17/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquired by plant parasitic nematodes that allow them to digest plant cell walls. Unlike the typical glycoside hydrolase (GH) family 5 cellulase genes which are found in several nematode species from the order Tylenchida, members of the GH45 cellulase have only been identified in a cluster including the families Parasitaphelenchidae (with the pinewood nematode Bursaphelenchus xylophilus) and Aphelenchoididae, and their origins remain unknown. RESULTS In order to investigate the distribution and evolution of GH45 cellulase genes in nematodes and fungi we performed a wide ranging screen for novel putative GH45 sequences. This revealed that the sequences are widespread mainly in Ascomycetous fungi and have so far been found in a single major nematode lineage. Close relationships between the sequences from nematodes and fungi were found through our phylogenetic analyses. An intron position is shared by sequences from Bursaphelenchus nematodes and several Ascomycetous fungal species. CONCLUSIONS The close phylogenetic relationships and conserved gene structure between the sequences from nematodes and fungi strongly supports the hypothesis that nematode GH45 cellulase genes were acquired via HGT from fungi. The rapid duplication and turnover of these genes within Bursaphelenchus genomes demonstrate that useful sequences acquired via HGT can become established in the genomes of recipient organisms and may open novel niches for these organisms to exploit.
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Affiliation(s)
- Juan E Palomares-Rius
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional, Apdo. 4084, 14080 Córdoba, Spain
| | - Yuuri Hirooka
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - Isheng J Tsai
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hayato Masuya
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Akina Hino
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Natsumi Kanzaki
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - John T Jones
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
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82
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Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJA, den Akker SEV, Holroyd N, Hunt M, Mantelin S, Naghra H, Pain A, Palomares-Rius JE, Zarowiecki M, Berriman M, Jones JT, Urwin PE. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol 2014; 15:R43. [PMID: 24580726 PMCID: PMC4054857 DOI: 10.1186/gb-2014-15-3-r43] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/03/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. RESULTS We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. CONCLUSIONS The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
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Affiliation(s)
- James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Taisei Kikuchi
- Forestry and Forest Products Research Institute, Tsukuba, Japan
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Thorpe
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Vivian Blok
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J A Cock
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Arnab Pain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan E Palomares-Rius
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Present address: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n Apdo 4084, 14080 Córdoba, Spain
| | - Magdalena Zarowiecki
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - John T Jones
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
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Abstract
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA
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84
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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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85
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Abstract
Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.
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Affiliation(s)
- Luis Boto
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales. CSIC, , C/ José Gutierrez Abascal 2, 28006 Madrid, Spain
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86
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Abstract
Secreted effectors represent the molecular interface between the nematode and its host plant. Studies that aimed at deciphering molecular plant-nematode interactions are hampered by technical hurdles that prevent the generation of transgenic nematodes. However, RNA interference (RNAi) has proven to be a valuable tool to specifically knock-down nematode effector genes, both ex planta and in planta. Plant-mediated RNAi of nematode genes not only facilitates functional characterization of effectors but also lends itself to a novel control strategy against plant-parasitic nematodes. Here, we describe currently used methods to silence genes in plant-parasitic cyst and root-knot nematodes.
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Affiliation(s)
- Axel A Elling
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA,
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87
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Goverse A, Smant G. The activation and suppression of plant innate immunity by parasitic nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:243-65. [PMID: 24906126 DOI: 10.1146/annurev-phyto-102313-050118] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant-parasitic nematodes engage in prolonged and intimate relationships with their host plants, often involving complex alterations in host cell morphology and function. It is puzzling how nematodes can achieve this, seemingly without activating the innate immune system of their hosts. Secretions released by infective juvenile nematodes are thought to be crucial for host invasion, for nematode migration inside plants, and for feeding on host cells. In the past, much of the research focused on the manipulation of developmental pathways in host plants by plant-parasitic nematodes. However, recent findings demonstrate that plant-parasitic nematodes also deliver effectors into the apoplast and cytoplasm of host cells to suppress plant defense responses. In this review, we describe the current insights in the molecular and cellular mechanisms underlying the activation and suppression of host innate immunity by plant-parasitic nematodes along seven critical evolutionary and developmental transitions in plant parasitism.
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Affiliation(s)
- Aska Goverse
- Laboratory of Nematology, Wageningen University, 6708 PD Wageningen, The Netherlands;
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88
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Kikuchi T, Cock PJ, Helder J, Jones JT. Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
While the majority of Aphelenchoides species are fungivorous, some species are plant parasites that have retained the ability to feed on fungi. Aphelenchoides besseyi is an important and widespread pathogen that causes ‘white tip’ disease on rice. This migratory endoparasitic nematode makes a significant contribution to the estimated $US 16 billion worth of damage caused by nematodes to rice crops. Here we describe a small-scale analysis of the transcriptome of A. besseyi. After sequencing, QC and assembly, approximately 5000 contigs were analysed. Bioinformatic analysis allowed 375 secreted proteins to be identified, including orthologues of proteins known to be secreted by other nematodes. One contig could encode an A. besseyi orthologue of a GHF45 cellulase, similar to those present in Bursaphelenchus xylophilus. No transcripts similar to GHF5 cellulases were present in this dataset.
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Affiliation(s)
- Tiasei Kikuchi
- 1Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan
| | - Peter J.A. Cock
- 2Cell and Molecular Sciences Group, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Johannes Helder
- 3Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John T. Jones
- 2Cell and Molecular Sciences Group, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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89
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Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jones MGK, Kikuchi T, Manzanilla-López R, Palomares-Rius JE, Wesemael WML, Perry RN. Top 10 plant-parasitic nematodes in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2013; 14:946-61. [PMID: 23809086 PMCID: PMC6638764 DOI: 10.1111/mpp.12057] [Citation(s) in RCA: 790] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.
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Affiliation(s)
- John T Jones
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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90
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Delay C, Imin N, Djordjevic MA. CEP genes regulate root and shoot development in response to environmental cues and are specific to seed plants. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5383-94. [PMID: 24179096 DOI: 10.1093/jxb/ert332] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The manifestation of repetitive developmental programmes during plant growth can be adjusted in response to various environmental cues. During root development, this means being able to precisely control root growth and lateral root development. Small signalling peptides have been found to play roles in many aspects of root development. One member of the CEP (C-TERMINALLY ENCODED PEPTIDE) gene family has been shown to arrest root growth. Here we report that CEP genes are widespread among seed plants but are not present in land plants that lack true branching roots or root vasculature. We have identified 10 additional CEP genes in Arabidopsis. Expression analysis revealed that CEP genes are regulated by environmental cues such as nitrogen limitation, increased salt levels, increased osmotic strength, and increased CO2 levels in both roots and shoots. Analysis of synthetic CEP variants showed that both peptide sequence and modifications of key amino acids affect CEP biological activity. Analysis of several CEP over-expression lines revealed distinct roles for CEP genes in root and shoot development. A cep3 knockout mutant showed increased root and shoot growth under a range of abiotic stress, nutrient, and light conditions. We demonstrate that CEPs are negative regulators of root development, slowing primary root growth and reducing lateral root formation. We propose that CEPs are negative regulators that mediate environmental influences on plant development.
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Affiliation(s)
- Christina Delay
- Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT 0200, Australia
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91
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Yang Y, Luo D. The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees. Evol Bioinform Online 2013; 9:453-66. [PMID: 24277980 PMCID: PMC3836563 DOI: 10.4137/ebo.s13032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.
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Affiliation(s)
- Yizi Yang
- School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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92
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Schönknecht G, Weber APM, Lercher MJ. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays 2013; 36:9-20. [DOI: 10.1002/bies.201300095] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Martin J. Lercher
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Institute for Computer Science; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
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93
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Gao C, Ren X, Mason AS, Liu H, Xiao M, Li J, Fu D. Horizontal gene transfer in plants. Funct Integr Genomics 2013; 14:23-9. [PMID: 24132513 DOI: 10.1007/s10142-013-0345-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 01/12/2023]
Abstract
Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries. HGT often occurs in microbic and eukaryotic genomes. However, the pathways by which HGTs occur in multicellular eukaryotes, especially in plants, are not well understood. We systematically summarized more than ten possible pathways for HGT. The intimate contact which frequently occurs in parasitism, symbiosis, pathogen, epiphyte, entophyte, and grafting interactions could promote HGTs between two species. Besides these direct transfer methods, genes can be exchanged with a vector as a bridge: possible vectors include pollen, fungi, bacteria, viruses, viroids, plasmids, transposons, and insects. HGT, especially when involving horizontal transfer of transposable elements, is recognized as a significant force propelling genomic variation and biological innovation, playing an important functional and evolutionary role in both eukaryotic and prokaryotic genomes. We proposed possible mechanisms by which HGTs can occur, which is useful in understanding the genetic information exchange among distant species or distant cellular components.
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Affiliation(s)
- Caihua Gao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, People's Republic of China
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94
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Luis P, Gauthier A, Trouvelot S, Poinssot B, Frettinger P. Identification of Plasmopara viticola genes potentially involved in pathogenesis on grapevine suggests new similarities between oomycetes and true fungi. PHYTOPATHOLOGY 2013; 103:1035-44. [PMID: 23634808 DOI: 10.1094/phyto-06-12-0121-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, these organisms share many common features during infection. We identified genes in the oomycete Plasmopara viticola that are potentially involved in pathogenesis in grapevine by using fungal databases and degenerate primers. Fragments of P. viticola genes encoding NADH-ubiquinone oxidoreductase (PvNuo), laccase (PvLac), and invertase (PvInv) were obtained. PvNuo was overexpressed at 2 days postinoculation (dpi), during the development of the first hyphal structures and haustoria. PvLac was overexpressed at 5 dpi when genes related to pterostilbene biosynthesis were induced in grapevine. Transcript level for PvInv increased between 1 and 4 dpi before reaching a plateau. These results might suggest a finely tuned strategy of infection depending on nutrition and plant response. Phylogenetic analyses of PvNuo showed that P. viticola clustered with other oomycetes and was associated with brown algae and diatoms, forming a typical Straminipila clade. Based on the comparison of available sequences for laccases and invertases, the group formed by P. viticola and other oomycetes tended to be more closely related to Opisthokonta than to Straminipila. Convergent evolution or horizontal gene transfer could explain the presence of fungus-like genes in P. viticola.
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95
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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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96
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Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 2013; 29:329-38. [DOI: 10.1016/j.pt.2013.05.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022]
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97
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Castagnone-Sereno P, Danchin EGJ, Perfus-Barbeoch L, Abad P. Diversity and evolution of root-knot nematodes, genus Meloidogyne: new insights from the genomic era. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:203-20. [PMID: 23682915 DOI: 10.1146/annurev-phyto-082712-102300] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Root-knot nematodes (RKNs) (Meloidogyne spp.) are obligate endoparasites of major worldwide economic importance. They exhibit a wide continuum of variation in their reproductive strategies, ranging from amphimixis to obligatory mitotic parthenogenesis. Molecular phylogenetic studies have highlighted divergence between mitotic and meiotic parthenogenetic RKN species and probable interspecific hybridization as critical steps in their speciation and diversification process. The recent completion of the genomes of two RKNs, Meloidogyne hapla and Meloidogyne incognita, that exhibit striking differences in their mode of reproduction (with and without sex, respectively), their geographic distribution, and their host range has opened the way for deciphering the evolutionary significance of (a)sexual reproduction in these parasites. Accumulating evidence suggests that whole-genome duplication (in M. incognita) and horizontal gene transfers (HGTs) represent major forces that have shaped the genome of current RKN species and may account for the extreme adaptive capacities and parasitic success of these nematodes.
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98
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Casacuberta E, González J. The impact of transposable elements in environmental adaptation. Mol Ecol 2013; 22:1503-17. [DOI: 10.1111/mec.12170] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 11/01/2012] [Accepted: 11/02/2012] [Indexed: 12/17/2022]
Affiliation(s)
- Elena Casacuberta
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Passeig Maritim de la Barceloneta 37-49 Barcelona 08003 Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Passeig Maritim de la Barceloneta 37-49 Barcelona 08003 Spain
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99
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Palomares-Rius JE, Hedley PE, Cock PJA, Morris JA, Jones JT, Vovlas N, Blok V. Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes. MOLECULAR PLANT PATHOLOGY 2012; 13:1120-34. [PMID: 22863280 PMCID: PMC6638826 DOI: 10.1111/j.1364-3703.2012.00821.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The potato cyst nematodes (PCNs) Globodera pallida and Globodera rostochiensis are important parasites of potato. PCNs undergo complex biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study was to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible and partially resistant potato genotypes. For this purpose, two microarray experiments were designed: (i) a comparison of eggs, infective second-stage juveniles (J2s) and sedentary parasitic-stage J2s (SJ2); (ii) a comparison of SJ2s at 8 days after inoculation (DAI) in the susceptible cultivar (Desirée) and two partially resistant lines. The results showed differential expression of G. pallida genes during the stages studied, including previously characterized effectors. In addition, a large number of genes changed their expression between SJ2s in the susceptible cultivar and those infecting partially resistant lines; the number of genes with modified expression was lower when the two partially resistant lines were compared. Moreover, a histopathological study was performed at several time points (7, 14 and 30 DAI) and showed the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison with the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison with those in the susceptible cultivar.
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Affiliation(s)
- Juan E Palomares-Rius
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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100
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Wybouw N, Balabanidou V, Ballhorn DJ, Dermauw W, Grbić M, Vontas J, Van Leeuwen T. A horizontally transferred cyanase gene in the spider mite Tetranychus urticae is involved in cyanate metabolism and is differentially expressed upon host plant change. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:881-889. [PMID: 22960016 DOI: 10.1016/j.ibmb.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 06/01/2023]
Abstract
The genome of the phytophagous two-spotted spider mite Tetranychus urticae was recently sequenced, representing the first complete chelicerate genome, but also the first genome of a highly polyphagous agricultural pest. Genome analysis revealed the presence of an unexpected high number of cases of putative horizontal gene transfers, including a gene that encodes a cyanase or cyanate lyase. In this study we show by recombinant expression that the T. urticae cyanase remained functionally active after horizontal gene transfer and has a high affinity for cyanate. Cyanases were also detected in other plant parasitic spider mites species such as Tetranychus evansi and Panonychus citri, suggesting that an ancient gene transfer occurred before the diversification within the Tetranychidae family. To investigate the potential role of cyanase in the evolution of plant parasitic spider mites, we studied cyanase expression patterns in T. urticae in relation to host plant range and cyanogenesis, a common plant defense mechanism. Spider mites can alter cyanase expression levels after transfer to several new host plants, including the cyanogenic Phaseolus lunatus. However, the role of cyanase is probably not restricted to cyanide response, but likely to the plant nutritional quality as a whole. We finally discuss potential interactions between cyanase activity and pyrimidine and amino acid synthesis.
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Affiliation(s)
- N Wybouw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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