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Lin CJ, Siddique S. Parasitic nematodes: dietary habits and their implications. Trends Parasitol 2024; 40:230-240. [PMID: 38262837 DOI: 10.1016/j.pt.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Nematodes, a diverse group of roundworms, exhibit a wide range of dietary habits, including parasitism of animals and plants. These parasites cause substantial economic losses in agriculture and pose significant health challenges to humans and animals. This review explores the unique adaptations of parasitic nematodes, emphasizing their nutritional requirements and metabolic dependencies. Recent research has identified cross-kingdom compartmentalization of vitamin B5 biosynthesis in some parasitic nematodes, shedding light on coevolutionary dynamics and potential targets for control strategies. Several open questions remain regarding the complexity of nematode nutrition, host manipulation, evolutionary adaptations, and the influence of environmental factors on their metabolic processes. Understanding these aspects offers promising avenues for targeted interventions to manage and control these economically and medically important parasites.
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Affiliation(s)
- Ching-Jung Lin
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
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2
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Pokhare SS, Thorpe P, Hedley P, Morris J, Habash SS, Elashry A, Eves-van den Akker S, Grundler FMW, Jones JT. Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1263-1274. [PMID: 32623778 DOI: 10.1111/tpj.14910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/18/2020] [Indexed: 05/03/2023]
Abstract
Interactions between plant-parasitic nematodes and their hosts are mediated by effectors, i.e. secreted proteins that manipulate the plant to the benefit of the pathogen. To understand the role of effectors in host adaptation in nematodes, we analysed the transcriptome of Heterodera sacchari, a cyst nematode parasite of rice (Oryza sativa) and sugarcane (Saccharum officinarum). A multi-gene phylogenetic analysis showed that H. sacchari and the cereal cyst nematode Heterodera avenae share a common evolutionary origin and that they evolved to parasitise monocot plants from a common dicot-parasitic ancestor. We compared the effector repertoires of H. sacchari with those of the dicot parasites Heterodera glycines and Globodera rostochiensis to understand the consequences of this transition. While, in general, effector repertoires are similar between the species, comparing effectors and non-effectors of H. sacchari and G. rostochiensis shows that effectors have accumulated more mutations than non-effectors. Although most effectors show conserved spatiotemporal expression profiles and likely function, some H. sacchari effectors are adapted to monocots. This is exemplified by the plant-peptide hormone mimics, the CLAVATA3/EMBRYO SURROUNDING REGION-like (CLE) effectors. Peptide hormones encoded by H. sacchari CLE effectors are more similar to those from rice than those from other plants, or those from other plant-parasitic nematodes. We experimentally validated the functional significance of these observations by demonstrating that CLE peptides encoded by H. sacchari induce a short root phenotype in rice, whereas those from a related dicot parasite do not. These data provide a functional example of effector evolution that co-occurred with the transition from a dicot-parasitic to a monocot-parasitic lifestyle.
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Affiliation(s)
- Somnath S Pokhare
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Peter Thorpe
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Pete Hedley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jennifer Morris
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Samer S Habash
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | - Abdelnaser Elashry
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | | | - Florian M W Grundler
- Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, 53115, Germany
| | - John T Jones
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
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3
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Kwon KM, Bekal S, Domier LL, Lambert KN. Active and inactive forms of biotin synthase occur in Heterodera glycines. J Nematol 2019; 51:e2019-69. [PMID: 34179812 PMCID: PMC6909392 DOI: 10.21307/jofnem-2019-069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 11/11/2022] Open
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), is a plant-parasitic nematode capable of manipulating host plant biochemistry and development. Many studies have suggested that the nematode has acquired genes from bacteria via horizontal gene transfer events (HGTs) that have the potential to enhance nematode parasitism. A recent allelic imbalance analysis identified two candidate virulence genes, which also appear to have entered the SCN genome through HGTs. One of the candidate genes, H. glycines biotin synthase (HgBioB), contained sequence polymorphisms between avirulent and virulent inbred SCN strains. To test the function of these HgBioB alleles, a complementation experiment using biotin synthase-deficient Escherichia coli was conducted. Here, we report that avirulent nematodes produce an active biotin synthase while virulent ones contain an inactive form of the enzyme. Moreover, sequencing analysis of HgBioB genes from SCN field populations indicates the presence of diverse mixture of HgBioB alleles with the virulent form being the most prevalent. We hypothesize that the mutations in the inactive HgBioB allele within the virulent SCN could result in a change in protein function that in some unknown way bolster its parasitic lifestyle.
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Affiliation(s)
- Khee Man Kwon
- Department of Crop Sciences, University of Illinois, Urbana, IL.,Department of Plant Pathology and Center for Applied Genetic Technologies, University of Georgia, Athens, GA
| | - Sadia Bekal
- Department of Agricultural and Biological Engineering, University of Illinois, Urbana, IL
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL.,United States Department of Agriculture - Agricultural Research Service, Urbana, IL
| | - Kris N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL
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Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG, Mimee B, den Akker SEV, Hudson M, Severin AJ, Baum TJ. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 2019; 20:119. [PMID: 30732586 PMCID: PMC6367775 DOI: 10.1186/s12864-019-5485-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. RESULTS Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons. CONCLUSIONS This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
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Affiliation(s)
- Rick Masonbrink
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Tom R. Maier
- Department of Plant Pathology, Iowa State University, Ames, IA USA
| | - Usha Muppirala
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Arun S. Seetharam
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Etienne Lord
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nathan T. Johnson
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA USA
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Matthew Hudson
- Department of Crop Sciences University of Illinois, Urbana, IL USA
| | | | - Thomas J. Baum
- Department of Plant Pathology, Iowa State University, Ames, IA USA
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Dunning Hotopp JC. Grafting or pruning in the animal tree: lateral gene transfer and gene loss? BMC Genomics 2018; 19:470. [PMID: 29914363 PMCID: PMC6006793 DOI: 10.1186/s12864-018-4832-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. RESULTS Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. CONCLUSIONS ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
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Affiliation(s)
- Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Danchin EGJ, Perfus-Barbeoch L, Rancurel C, Thorpe P, Da Rocha M, Bajew S, Neilson R, Guzeeva ES, Da Silva C, Guy J, Labadie K, Esmenjaud D, Helder J, Jones JT, den Akker SEV. The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. Genes (Basel) 2017; 8:genes8100287. [PMID: 29065523 PMCID: PMC5664137 DOI: 10.3390/genes8100287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 11/16/2022] Open
Abstract
Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.
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Affiliation(s)
- Etienne G J Danchin
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | | | - Corinne Rancurel
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Peter Thorpe
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Martine Da Rocha
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Simon Bajew
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Roy Neilson
- Ecological Sciences Group, IPM@Hutton, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Elena Sokolova Guzeeva
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
- Centre of Parasitology of the A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia.
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Julie Guy
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 92057, Evry, France.
| | - Daniel Esmenjaud
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis Cedex, France.
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
- School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9TZ, UK.
| | - Sebastian Eves-van den Akker
- Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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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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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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Duceppe MO, Lafond-Lapalme J, Palomares-Rius JE, Sabeh M, Blok V, Moffett P, Mimee B. Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida. Sci Rep 2017. [PMID: 28634407 PMCID: PMC5478601 DOI: 10.1038/s41598-017-03871-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Potato cyst nematodes (PCNs), Globodera rostochiensis and G. pallida, cause important economic losses. They are hard to manage because of their ability to remain dormant in soil for many years. Although general knowledge about these plant parasitic nematodes has considerably increased over the past decades, very little is known about molecular events involved in cyst dormancy and hatching, two key steps of their development. Here, we have studied the progression of PCN transcriptomes from dry cysts to hatched juveniles using RNA-Seq. We found that several cell detoxification-related genes were highly active in the dry cysts. Many genes linked to an increase of calcium and water uptake were up-regulated during transition from dormancy to hydration. Exposure of hydrated cysts to host plant root exudates resulted in different transcriptional response between species. After 48 h of exposure, G. pallida cysts showed no significant modulation of gene expression while G. rostochiensis had 278 differentially expressed genes. The first G. rostochiensis significantly up-regulated gene was observed after 8 h and was coding for a transmembrane metalloprotease. This enzyme is able to activate/inactivate peptide hormones and could be involved in a cascade of events leading to hatching. Several known effector genes were also up-regulated during hatching.
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Affiliation(s)
- Marc-Olivier Duceppe
- Agriculture and Agri-Food Canada, 430, Boulevard Gouin Saint-Jean-sur-Richelieu (Québec), J3B 3E6, Québec, Canada.,Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield (OLF), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada
| | - Joël Lafond-Lapalme
- Agriculture and Agri-Food Canada, 430, Boulevard Gouin Saint-Jean-sur-Richelieu (Québec), J3B 3E6, Québec, Canada.,Département de Biologie, Université de Sherbrooke, Sherbrooke, J1K 2R1, Canada
| | - Juan Emilio Palomares-Rius
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom.,Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
| | - Michaël Sabeh
- Agriculture and Agri-Food Canada, 430, Boulevard Gouin Saint-Jean-sur-Richelieu (Québec), J3B 3E6, Québec, Canada
| | - Vivian Blok
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
| | - Peter Moffett
- Département de Biologie, Université de Sherbrooke, Sherbrooke, J1K 2R1, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, 430, Boulevard Gouin Saint-Jean-sur-Richelieu (Québec), J3B 3E6, Québec, Canada.
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11
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Gagat P, Mackiewicz P. Cymbomonas tetramitiformis - a peculiar prasinophyte with a taste for bacteria sheds light on plastid evolution. Symbiosis 2016; 71:1-7. [PMID: 28066124 PMCID: PMC5167767 DOI: 10.1007/s13199-016-0464-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022]
Abstract
Cymbomonas tetramitiformis is a peculiar green alga that unites in one cell the abilities of photosynthesis and phagocytosis, which makes it a very useful model for the study of the evolution of plastid endosymbiosis. We have pondered over this issue and propose an evolutionary scenario of trophic strategies in eukaryotes, including primary and secondary plastid endosymbioses. C. tetramitiformis is a prototroph, just like the common ancestor of Archaeplastida was, and can synthesize most small organic molecules contrary to other eukaryotic phagotrophs, e.g. some metazoans, amoebozoans, and ciliates, which have not evolved tight endosymbiotic relationships. In order to establish a permanent photosynthetic endosymbiont they do not have to become prototrophs, but have to acquire the genes necessary for plastid retention via horizontal (including endosymbiotic) gene transfer. Such processes occurred successfully in the ancestors of eukaryotes with permanent secondary plastids and thus led to their great diversification. The preservation of phagocytosis in Cymbomonas (and some other prasinophytes as well) seems to result from nutrient deficiency in their oligotrophic habitats. This forces them to supplement their diet with phagocytized prey, in contrasts to the thecate amoeba Paulinella chromatophora, which also successfully transformed cyanobacteria into permanent organelles. Although Paulinella endosymbionts were acquired very recently in comparison to primary plastids, Paulinella has lost the ability to phagocytose, most probably due to the fact that it inhabits nutrient-rich environments, which renders the phagotrophy nonessential.
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Affiliation(s)
- Przemysław Gagat
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383 Wrocław, Poland
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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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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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Bekal S, Domier LL, Gonfa B, Lakhssassi N, Meksem K, Lambert KN. A SNARE-Like Protein and Biotin Are Implicated in Soybean Cyst Nematode Virulence. PLoS One 2015; 10:e0145601. [PMID: 26714307 PMCID: PMC4699853 DOI: 10.1371/journal.pone.0145601] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 12/07/2015] [Indexed: 11/24/2022] Open
Abstract
Phytoparasitic nematodes that are able to infect and reproduce on plants that are considered resistant are referred to as virulent. The mechanism(s) that virulent nematodes employ to evade or suppress host plant defenses are not well understood. Here we report the use of a genetic strategy (allelic imbalance analysis) to associate single nucleotide polymorphisms (SNPs) with nematode virulence genes in Heterodera glycines, the soybean cyst nematode (SCN). To accomplish this analysis, a custom SCN SNP array was developed and used to genotype SCN F3-derived populations grown on resistant and susceptible soybean plants. Three SNPs reproducibly showed allele imbalances between nematodes grown on resistant and susceptible plants. Two candidate SCN virulence genes that were tightly linked to the SNPs were identified. One SCN gene encoded biotin synthase (HgBioB), and the other encoded a bacterial-like protein containing a putative SNARE domain (HgSLP-1). The two genes mapped to two different linkage groups. HgBioB contained sequence polymorphisms between avirulent and virulent nematodes. However, the gene encoding HgSLP-1 had reduced copy number in virulent nematode populations and appears to produce multiple forms of the protein via intron retention and alternative splicing. We show that HgSLP-1 is an esophageal-gland protein that is secreted by the nematode during plant parasitism. Furthermore, in bacterial co-expression experiments, HgSLP-1 co-purified with the SCN resistance protein Rhg1 α-SNAP, suggesting that these two proteins physically interact. Collectively our data suggest that multiple SCN genes are involved in SCN virulence, and that HgSLP-1 may function as an avirulence protein and when absent it helps SCN evade host defenses.
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Affiliation(s)
- Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Biruk Gonfa
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
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Bekal S, Domier LL, Gonfa B, McCoppin NK, Lambert KN, Bhalerao K. A novel flavivirus in the soybean cyst nematode. J Gen Virol 2014; 95:1272-1280. [PMID: 24643877 DOI: 10.1099/vir.0.060889-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), is a subterranean root pathogen that causes the most damaging disease of soybean in the USA. A novel nematode virus genome, soybean cyst nematode virus 5 (SbCNV-5), was identified in RNA sequencing data from SCN eggs and second-stage juveniles. The SbCNV-5 RNA-dependent RNA polymerase and RNA helicase domains had homology to pestiviruses in the family Flaviviridae, suggesting that SbCNV-5 is a positive-polarity ssRNA virus. SbCNV-5 RNA was present in all nematode developmental stages, indicating a transovarial mode of transmission, but is also potentially sexually transmitted via the male. SbCNV-5 was common in SCN laboratory cultures and in nematode populations isolated from the field. Transmission electron microscopy of sections from a female SCN showed virus particles budding from the endoplasmic reticulum and in endosomes. The size of the viral genome was 19 191 nt, which makes it much larger than other known pestiviruses. Additionally, the presence of a methyltransferase in the SbCNV-5 genome is atypical for a pestivirus. When cDNA sequences were mapped to the genome of SbCNV-5, a disproportionate number aligned to the 3' NTR, suggesting that SbCNV-5 produces a subgenomic RNA, which was confirmed by RNA blot analysis. As subgenomic RNAs and methyltransferases do not occur in pestiviruses, we conclude that SbCNV-5 is a new flavivirus infecting SCNs.
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Affiliation(s)
- Sadia Bekal
- Department of Agricultural and Biological Engineering, University of Illinois, Urbana, IL 61810, USA
| | - Leslie L Domier
- US Department of Agriculture, Agricultural Research Service, University of Illinois, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Biruk Gonfa
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Nancy K McCoppin
- US Department of Agriculture, Agricultural Research Service, University of Illinois, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Kris N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Kaustubh Bhalerao
- Department of Agricultural and Biological Engineering, University of Illinois, Urbana, IL 61810, USA
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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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17
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Affiliation(s)
- Peter Gahan
- Anatomy & Human Sciences; King's College London; London Bridge London SE1 1UL UK
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18
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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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Hansen AK, Moran NA. The impact of microbial symbionts on host plant utilization by herbivorous insects. Mol Ecol 2013; 23:1473-1496. [PMID: 23952067 DOI: 10.1111/mec.12421] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/02/2013] [Accepted: 06/12/2013] [Indexed: 01/18/2023]
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Helliwell KE, Wheeler GL, Smith AG. Widespread decay of vitamin-related pathways: coincidence or consequence? Trends Genet 2013; 29:469-78. [DOI: 10.1016/j.tig.2013.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/09/2013] [Accepted: 03/25/2013] [Indexed: 02/03/2023]
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Pauchet Y, Heckel DG. The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc Biol Sci 2013; 280:20131021. [PMID: 23698014 DOI: 10.1098/rspb.2013.1021] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae, possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.
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Affiliation(s)
- Yannick Pauchet
- Department of Entomology, Max Planck institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany.
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22
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Characterization of an ancient lepidopteran lateral gene transfer. PLoS One 2013; 8:e59262. [PMID: 23533610 PMCID: PMC3606386 DOI: 10.1371/journal.pone.0059262] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/13/2013] [Indexed: 02/03/2023] Open
Abstract
Bacteria to eukaryote lateral gene transfers (LGT) are an important potential source of material for the evolution of novel genetic traits. The explosion in the number of newly sequenced genomes provides opportunities to identify and characterize examples of these lateral gene transfer events, and to assess their role in the evolution of new genes. In this paper, we describe an ancient lepidopteran LGT of a glycosyl hydrolase family 31 gene (GH31) from an Enterococcus bacteria. PCR amplification between the LGT and a flanking insect gene confirmed that the GH31 was integrated into the Bombyx mori genome and was not a result of an assembly error. Database searches in combination with degenerate PCR on a panel of 7 lepidopteran families confirmed that the GH31 LGT event occurred deep within the Order approximately 65–145 million years ago. The most basal species in which the LGT was found is Plutella xylostella (superfamily: Yponomeutoidea). Array data from Bombyx mori shows that GH31 is expressed, and low dN/dS ratios indicates the LGT coding sequence is under strong stabilizing selection. These findings provide further support for the proposition that bacterial LGTs are relatively common in insects and likely to be an underappreciated source of adaptive genetic material.
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Lopez-Nicora HD, Craig JP, Gao X, Lambert KN, Niblack TL. Evaluation of Cultivar Resistance to Soybean Cyst Nematode with a Quantitative Polymerase Chain Reaction Assay. PLANT DISEASE 2012; 96:1556-1563. [PMID: 30727319 DOI: 10.1094/pdis-12-11-1083-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, is a major pathogen of soybean. Effective management of this pathogen is contingent on the use of resistant cultivars; thus, screening for resistant cultivars is essential. The purpose of this research was to develop a method to assess infection of soybean roots by H. glycines with real-time quantitative polymerase chain reaction (qPCR). This method will serve as a prelude to differentiation of resistance levels in soybean cultivars. A reproducible inoculation method was developed by means of a sand column to provide active second-stage juveniles (J2). Two-day-old soybean roots were infested with 0 or 1,000 J2/ml distilled water per seedling. Twenty-four hours after infestation, the roots were surface-sterilized and genomic DNA (gDNA) was extracted. For the qPCR assay, a primer pair for the single copy gene HgSNO, which codes for a protein involved in the production of vitamin B6, was selected for H. glycines gDNA amplification within soybean roots. Compatible 'Lee 74', incompatible 'Peking', and cultivars with different levels of resistance to H. glycines were infested with 0 or 1,000 J2/ml distilled water per seedling. Twenty-four hours postinfestation, infected seedlings were transplanted into pasteurized soil. Subsequently, they were harvested at 1, 7, 10, 14, and 21 days postinfestation for gDNA extraction. With the qPCR assay, the time needed to differentiate highly resistant cultivars from the rest was reduced. Quantification of H. glycines infection by traditional means (numbers of females produced in 30 days) is a time-consuming practice. This qPCR assay has the potential to replace the traditional Female Index-based screening and improve precision in determining infection levels.
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Affiliation(s)
| | - James P Craig
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley 94720
| | - Xuebiao Gao
- Pasteuria Bioscience, Inc. 12085 Research Drive, Suite 185 Alachua, FL 32615
| | - Kris N Lambert
- Department of Crop Science, University of Illinois, Urbana 61801
| | - Terry L Niblack
- Department of Plant Pathology, Ohio State University, Columbus 43210
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Ni T, Yue J, Sun G, Zou Y, Wen J, Huang J. Ancient gene transfer from algae to animals: mechanisms and evolutionary significance. BMC Evol Biol 2012; 12:83. [PMID: 22690978 PMCID: PMC3494510 DOI: 10.1186/1471-2148-12-83] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 06/01/2012] [Indexed: 11/30/2022] Open
Abstract
Background Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution.
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Affiliation(s)
- Ting Ni
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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Ramulu HG, Raoult D, Pontarotti P. The rhizome of life: what about metazoa? Front Cell Infect Microbiol 2012; 2:50. [PMID: 22919641 PMCID: PMC3417402 DOI: 10.3389/fcimb.2012.00050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/23/2012] [Indexed: 02/03/2023] Open
Abstract
The increase in huge number of genomic sequences in recent years has contributed to various genetic events such as horizontal gene transfer (HGT), gene duplication and hybridization of species. Among them HGT has played an important role in the genome evolution and was believed to occur only in Bacterial and Archaeal genomes. As a result, genomes were found to be chimeric and the evolution of life was represented in different forms such as forests, networks and species evolution was described more like a rhizome, rather than a tree. However, in the last few years, HGT has also been evidenced in other group such as metazoa (for example in root-knot nematodes, bdelloid rotifers and mammals). In addition to HGT, other genetic events such as transfer by retrotransposons and hybridization between more closely related lineages are also well established. Therefore, in the light of such genetic events, whether the evolution of metazoa exists in the form of a tree, network or rhizome is highly questionable and needs to be determined. In the current review, we will focus on the role of HGT, retrotransposons and hybridization in the metazoan evolution.
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Affiliation(s)
- Hemalatha G. Ramulu
- LATP UMR-CNRS 7353, Evolution Biologique et Modélisation, Aix-Marseille UniversitéeMarseille, France
- URMITE CNRS-IRD UMR6236-198Marseille, France
| | | | - Pierre Pontarotti
- LATP UMR-CNRS 7353, Evolution Biologique et Modélisation, Aix-Marseille UniversitéeMarseille, France
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Haegeman A, Jones JT, Danchin EGJ. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:879-87. [PMID: 21539433 DOI: 10.1094/mpmi-03-11-0055] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The origin of plant parasitism within the phylum Nematoda is intriguing. The ability to parasitize plants has originated independently at least three times during nematode evolution and, as more molecular data has emerged, it has become clear that multiple instances of horizontal gene transfer (HGT) from bacteria and fungi have played a crucial role in the nematode's adaptation to this new lifestyle. The first reported HGT cases in plant-parasitic nematodes were genes encoding plant cell wall-degrading enzymes. Other putative examples of HGT were subsequently described, including genes that may be involved in the modulation of the plant's defense system, the establishment of a nematode feeding site, and the synthesis or processing of nutrients. Although, in many cases, it is difficult to pinpoint the donor organism, candidate donors are usually soil dwelling and are either plant-pathogenic or plant-associated microorganisms, hence occupying the same ecological niche as the nematodes. The exact mechanisms of transfer are unknown, although close contacts with donor microorganisms, such as symbiotic or trophic interactions, are a possibility. The widespread occurrence of horizontally transferred genes in evolutionarily independent plant-parasitic nematode lineages suggests that HGT may be a prerequisite for successful plant parasitism in nematodes.
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
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Bekal S, Domier LL, Niblack TL, Lambert KN. Discovery and initial analysis of novel viral genomes in the soybean cyst nematode. J Gen Virol 2011; 92:1870-1879. [PMID: 21490246 DOI: 10.1099/vir.0.030585-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nematodes are the most abundant multicellular animals on earth, yet little is known about their natural viral pathogens. To date, only two nematode virus genomes have been reported. Consequently, nematode viruses have been overlooked as important biotic factors in the study of nematode ecology. Here, we show that one plant parasitic nematode species, Heterodera glycines, the soybean cyst nematode (SCN), harbours four different RNA viruses. The nematode virus genomes were discovered in the SCN transcriptome after high-throughput sequencing and assembly. All four viruses have negative-sense RNA genomes, and are distantly related to nyaviruses and bornaviruses, rhabdoviruses, bunyaviruses and tenuiviruses. Some members of these families replicate in and are vectored by insects, and can cause significant diseases in animals and plants. The novel viral sequences were detected in both eggs and the second juvenile stage of SCN, suggesting that these viruses are transmitted vertically. While there was no evidence of integration of viral sequences into the nematode genome, we indeed detected transcripts from these viruses by using quantitative PCR. These data are the first finding of virus genomes in parasitic nematodes. This discovery highlights the need for further exploration for nematode viruses in all tropic groups of these diverse and abundant animals, to determine how the presence of these viruses affects the fitness of the nematode, strategies of viral transmission and mechanisms of viral pathogenesis.
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Affiliation(s)
- Sadia Bekal
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Leslie L Domier
- United States Department of Agriculture, Agricultural Research Service, Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Terry L Niblack
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
| | - Kris N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL 61810, USA
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Horizontal gene transfer between bacteria and animals. Trends Genet 2011; 27:157-63. [PMID: 21334091 DOI: 10.1016/j.tig.2011.01.005] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/21/2011] [Accepted: 01/21/2011] [Indexed: 12/31/2022]
Abstract
Horizontal gene transfer is increasingly described between bacteria and animals. Such transfers that are vertically inherited have the potential to influence the evolution of animals. One classic example is the transfer of DNA from mitochondria and chloroplasts to the nucleus after the acquisition of these organelles by eukaryotes. Even today, many of the described instances of bacteria-to-animal transfer occur as part of intimate relationships such as those of endosymbionts and their invertebrate hosts, particularly insects and nematodes, while numerous transfers are also found in asexual animals. Both of these observations are consistent with modern evolutionary theory, in particular the serial endosymbiotic theory and Muller's ratchet. Although it is tempting to suggest that these particular lifestyles promote horizontal gene transfer, it is difficult to ascertain given the nonrandom sampling of animal genome sequencing projects and the lack of a systematic analysis of animal genomes for such transfers.
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Transcript analysis of parasitic females of the sedentary semi-endoparasitic nematode Rotylenchulus reniformis. Mol Biochem Parasitol 2010; 172:31-40. [PMID: 20346373 DOI: 10.1016/j.molbiopara.2010.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/12/2010] [Accepted: 03/15/2010] [Indexed: 10/19/2022]
Abstract
Rotylenchulus reniformis, the reniform nematode, is a sedentary semi-endoparasitic nematode capable of infecting >300 plant species, including a large number of crops such as cotton, soybean, and pineapple. In contrast to other economically important plant-parasitic nematodes, molecular genetic data regarding the R. reniformis transcriptome is virtually nonexistant. Herein, we present a survey of R. reniformis ESTs that were sequenced from a sedentary parasitic female cDNA library. Cluster analysis of 2004 high quality ESTs produced 123 contigs and 508 singletons for a total of 631 R. reniformis unigenes. BLASTX analyses revealed that 39% of all unigenes showed similarity to known proteins (E<or=1.0e-04). R. reniformis genes homologous to known parasitism genes were identified and included beta-1,4-endoglucanase, fatty acid- and retinol-binding proteins, and an esophageal gland cell-specific gene from Heterodera glycines. Furthermore, a putative ortholog of an enzyme involved in thiamin biosynthesis, thought to exist solely in prokaryotes, fungi, and plants, was identified. Lastly, 114 R. reniformis unigenes orthologous to RNAi-lethal Caenorhabditis elegans genes were discovered. The work described here offers a glimpse into the transcriptome of a sedentary semi-endoparasitic nematode which (i) provides the transcript sequence data necessary for investigating engineered resistance against R. reniformis and (ii) hints at the existance of a thiamin biosynthesis pathway in an animal.
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Abstract
The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.
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Affiliation(s)
- Jan O Andersson
- Department of Evolution, Genomics and Systematics, Uppsala University, Uppsala S-752 36, Sweden.
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Nedelcu AM, Blakney AJC, Logue KD. Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention. J Evol Biol 2009; 22:1882-94. [PMID: 19619164 DOI: 10.1111/j.1420-9101.2009.01797.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.
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Affiliation(s)
- A M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB, Canada.
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Neuwirth M, Strohmeier M, Windeisen V, Wallner S, Deller S, Rippe K, Sinning I, Macheroux P, Tews I. X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases. FEBS Lett 2009; 583:2179-86. [PMID: 19523954 DOI: 10.1016/j.febslet.2009.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
Abstract
The universal enzymatic cofactor vitamin B6 can be synthesized as pyridoxal 5-phosphate (PLP) by the glutamine amidotransferase Pdx1. We show that Saccharomyces cerevisiae Pdx1 is hexameric by analytical ultracentrifugation and by crystallographic 3D structure determination. Bacterial homologues were previously reported to exist in hexamer:dodecamer equilibrium. A small sequence insertion found in yeast Pdx1 elevates the dodecamer dissociation constant when introduced into Bacillus subtilis Pdx1. Further, we demonstrate that the yeast Pdx1 C-terminus contacts an adjacent subunit, and deletion of this segment decreases enzymatic activity 3.5-fold, suggesting a role in catalysis.
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Affiliation(s)
- Martina Neuwirth
- Technische Universität Graz, Institut für Biochemie, Graz, Austria
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Rosso MN, Jones JT, Abad P. RNAi and functional genomics in plant parasitic nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2009; 47:207-32. [PMID: 19400649 DOI: 10.1146/annurev.phyto.112408.132605] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant nematology is currently undergoing a revolution with the availability of the first genome sequences as well as comprehensive expressed sequence tag (EST) libraries from a range of nematode species. Several strategies are being used to exploit this wealth of information. Comparative genomics is being used to explore the acquisition of novel genes associated with parasitic lifestyles. Functional analyses of nematode genes are moving toward larger scale studies including global transcriptome profiling. RNA interference (RNAi) has been shown to reduce expression of a range of plant parasitic nematode genes and is a powerful tool for functional analysis of nematode genes. RNAi-mediated suppression of genes essential for nematode development, survival, or parasitism is revealing new targets for nematode control. Plant nematology in the genomics era is now facing the challenge to develop RNAi screens adequate for high-throughput functional analyses.
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Affiliation(s)
- M N Rosso
- INRA, UNSA, UMR 1301, CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, F-06903 Sophia Antipolis, France.
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