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Mwaka HS, Bauters L, Namaganda J, Marcou S, Bwesigye PN, Kubiriba J, Smagghe G, Tushemereirwe WK, Gheysen G. Transgenic East African Highland Banana Plants Are Protected against Radopholus similis through Host-Delivered RNAi. Int J Mol Sci 2023; 24:12126. [PMID: 37569502 PMCID: PMC10418933 DOI: 10.3390/ijms241512126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The burrowing nematode Radopholus similis is considered a major problem of intensive banana cultivation. It can cause extensive root damage resulting in the toppling disease of banana, which means that plants fall to the ground. Soaking R. similis in double-stranded (ds) RNA of the nematode genes Rps13, chitin synthase (Chs-2), Unc-87, Pat-10 or beta-1,4-endoglucanase (Eng1a) suppressed reproduction on carrot discs, from 2.8-fold (Chs-2) to 7-fold (Rps13). The East African Highland Banana cultivar Nakitembe was then transformed with constructs for expression of dsRNA against the same genes, and for each construct, 30 independent transformants were tested with nematode infection. Four months after transfer from in vitro culture to the greenhouse, the banana plants were transferred to a screenhouse and inoculated with 2000 nematodes per plant, and thirteen weeks later, they were analyzed for several parameters including plant growth, root necrosis and final nematode population. Plants with dsRNA constructs against the nematode genes were on average showing lower nematode multiplication and root damage than the nontransformed controls or the banana plants expressing dsRNA against the nonendogenous gene. In conclusion, RNAi seems to efficiently protect banana against damage caused by R. similis, opening perspectives to control this pest.
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Affiliation(s)
- Henry Shaykins Mwaka
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Lander Bauters
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
| | - Josephine Namaganda
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Shirley Marcou
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
| | - Priver Namanya Bwesigye
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Jerome Kubiriba
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Guy Smagghe
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
| | | | - Godelieve Gheysen
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
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2
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Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, Shao J, Koutsovoulos GD, Zasada I, Matsumoto T, Danchin EGJ, Baum TJ, Eves-van den Akker S, Nemchinov LG. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathog 2021; 17:e1010036. [PMID: 34748609 PMCID: PMC8601627 DOI: 10.1371/journal.ppat.1010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/18/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Roxana Y. Myers
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Clement Pellegrin
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Wram
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Cedar Hesse
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Thomas R. Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Jonathan Shao
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | | | - Inga Zasada
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Tracie Matsumoto
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Etienne G. J. Danchin
- INRAE, Université Côte d’Azur, CNRS, Institute Sophia Agrobiotech, Sophia Antipolis, France
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | | | - Lev G. Nemchinov
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
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3
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Lefoulon E, Foster JM, Truchon A, Carlow CKS, Slatko BE. The Wolbachia Symbiont: Here, There and Everywhere. Results Probl Cell Differ 2021; 69:423-451. [PMID: 33263882 DOI: 10.1007/978-3-030-51849-3_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wolbachia symbionts, first observed in the 1920s, are now known to be present in about 30-70% of tested arthropod species, in about half of tested filarial nematodes (including the majority of human filarial nematodes), and some plant-parasitic nematodes. In arthropods, they are generally viewed as parasites while in nematodes they appear to be mutualists although this demarcation is not absolute. Their presence in arthropods generally leads to reproductive anomalies, while in nematodes, they are generally required for worm development and reproduction. In mosquitos, Wolbachia inhibit RNA viral infections, leading to populational reductions in human RNA virus pathogens, whereas in filarial nematodes, their requirement for worm fertility and survival has been channeled into their use as drug targets for filariasis control. While much more research on these ubiquitous symbionts is needed, they are viewed as playing significant roles in biological processes, ranging from arthropod speciation to human health.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Jeremy M Foster
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Alex Truchon
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - C K S Carlow
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Barton E Slatko
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA.
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4
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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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5
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Mathew R, Opperman CH. Current Insights into Migratory Endoparasitism: Deciphering the Biology, Parasitism Mechanisms, and Management Strategies of Key Migratory Endoparasitic Phytonematodes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E671. [PMID: 32466416 PMCID: PMC7356796 DOI: 10.3390/plants9060671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 01/12/2023]
Abstract
Despite their physiological differences, sedentary and migratory plant-parasitic nematodes (PPNs) share several commonalities. Functional characterization studies of key effectors and their targets identified in sedentary phytonematodes are broadly applied to migratory PPNs, generalizing parasitism mechanisms existing in distinct lifestyles. Despite their economic significance, host-pathogen interaction studies of migratory endoparasitic nematodes are limited; they have received little attention when compared to their sedentary counterparts. Because several migratory PPNs form disease complexes with other plant-pathogens, it is important to understand multiple factors regulating their feeding behavior and lifecycle. Here, we provide current insights into the biology, parasitism mechanism, and management strategies of the four-key migratory endoparasitic PPN genera, namely Pratylenchus, Radopholus, Ditylenchus, and Bursaphelenchus. Although this review focuses on these four genera, many facets of feeding mechanisms and management are common across all migratory PPNs and hence can be applied across a broad genera of migratory phytonematodes.
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Affiliation(s)
| | - Charles H. Opperman
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA;
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6
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RNA-Seq revealed that infection with white tip nematodes could downregulate rice photosynthetic genes. Funct Integr Genomics 2019; 20:367-381. [DOI: 10.1007/s10142-019-00717-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
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7
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Mathew R, Burke M, Opperman CH. A Draft Genome Sequence of the Burrowing Nematode Radopholus similis. J Nematol 2019; 51:e2019-51. [PMID: 34179801 PMCID: PMC6909026 DOI: 10.21307/jofnem-2019-051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Radopholus similis also known as the burrowing nematode is a devastating pest of banana (Musa spp.) and many economically important crops and ornamentals. In this publication, we present the genome assembly of R. similis.
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Affiliation(s)
- Reny Mathew
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Mark Burke
- Accelerated Technologies Laboratories, Inc., West End, NC
| | - Charles H Opperman
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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8
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Wram CL, Hesse CN, Wasala SK, Howe DK, Peetz AB, Denver DR, Humphreys-Pereira D, Zasada IA. Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica. J Nematol 2019; 51:e2019-52. [PMID: 34179798 PMCID: PMC6909021 DOI: 10.21307/jofnem-2019-052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Radopholus similis is an economically important pest of both banana and citrus in tropical regions. Here we present draft genomes from two populations of R. similis from Costa Rica that were created and assembled using short read libraries from Illumina HiSeq technology.
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Affiliation(s)
- Catherine L Wram
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Cedar N Hesse
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
| | - Sulochana K Wasala
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Danny Humphreys-Pereira
- Laboratorio de Nematología, Centro de Investigación en Protección de Cultivos, Escuela de Agronomía, Universidad de Costa Rica, San Jose, Costa Rica, 2060
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
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9
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Huang X, Xu CL, Yang SH, Li JY, Wang HL, Zhang ZX, Chen C, Xie H. Life-stage specific transcriptomes of a migratory endoparasitic plant nematode, Radopholus similis elucidate a different parasitic and life strategy of plant parasitic nematodes. Sci Rep 2019; 9:6277. [PMID: 31000750 PMCID: PMC6472380 DOI: 10.1038/s41598-019-42724-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/02/2019] [Indexed: 01/21/2023] Open
Abstract
Radopholus similis is an important migratory endoparasitic nematode, severely harms banana, citrus and many other commercial crops. Little is known about the molecular mechanism of infection and pathogenesis of R. similis. In this study, 64761 unigenes were generated from eggs, juveniles, females and males of R. similis. 11443 unigenes showed significant expression difference among these four life stages. Genes involved in host parasitism, anti-host defense and other biological processes were predicted. There were 86 and 102 putative genes coding for cell wall degrading enzymes and antioxidase respectively. The amount and type of putative parasitic-related genes reported in sedentary endoparasitic plant nematodes are variable from those of migratory parasitic nematodes on plant aerial portion. There were no sequences annotated to effectors in R. similis, involved in feeding site formation of sedentary endoparasites nematodes. This transcriptome data provides a new insight into the parasitic and pathogenic molecular mechanisms of the migratory endoparasitic nematodes. It also provides a broad idea for further research on R. similis.
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Affiliation(s)
- Xin Huang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Chun-Ling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Si-Hua Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Jun-Yi Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Hong-Le Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zi-Xu Zhang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
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10
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Li JY, Chen WZ, Yang SH, Xu CL, Huang X, Chen C, Xie H. Screening of reference genes in real-time PCR for Radopholus similis. PeerJ 2019; 7:e6253. [PMID: 30671304 PMCID: PMC6339476 DOI: 10.7717/peerj.6253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Six candidate reference genes were chosen from the transcriptome database of Radopholus similis using the bioinformatics method, including four conventional reference genes (actin, Eukaryotic translation initiation factor 5A (eIF5A), Tubulin alpha (a-tubulin), ubiquitin (UBI)) and two new candidate reference genes (Ribosomal protein S21 (Rps21) and Serine/threonine protein phosphatase PP1-β catalytic subunit (β-PP1)). In addition, a traditional reference gene 18S ribosomal RNA (18S rRNA) obtained from NCBI databases was also added to the analysis. Real-time PCR was used to detect the expression of seven candidate reference genes in six populations of R. similis and four developmental stages (female, male, larva and egg) of a population. The stability of the expression of candidate genes was evaluated by three software programs, BestKeeper, geNorm and NormFinder. The results showed that eIF5A is the most suitable reference gene for gene functional research of different populations, while both Rps21 and eIF5A are the most suitable reference genes for different developmental stages of a population. Therefore, eIF5A is the best reference gene for studying R. similis. However, one defect of this study is that only seven candidate reference genes were analyzed; ideally, more genes should be tested.
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Affiliation(s)
- Jun-Yi Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Wan-Zhu Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Si-Hua Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Chun-Ling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xin Huang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
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11
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Vieira P, Maier TR, Eves‐van den Akker S, Howe DK, Zasada I, Baum TJ, Eisenback JD, Kamo K. Identification of candidate effector genes of Pratylenchus penetrans. MOLECULAR PLANT PATHOLOGY 2018; 19:1887-1907. [PMID: 29424950 PMCID: PMC6638058 DOI: 10.1111/mpp.12666] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 05/02/2023]
Abstract
Pratylenchus penetrans is one of the most important species of root lesion nematodes (RLNs) because of its detrimental and economic impact in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbours a significant number of secreted proteins that play key roles during parasitism. Here, we combined spatially and temporally resolved next-generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the oesophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen.
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Affiliation(s)
- Paulo Vieira
- Department of Plant Pathology, Physiology, and Weed ScienceVirginia TechBlacksburgVA 24061USA
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of AgricultureBeltsvilleMD 20705‐2350USA
| | - Thomas R. Maier
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | - Sebastian Eves‐van den Akker
- Department of Biological ChemistryJohn Innes Centre, Norwich Research ParkNorwich NR4 7UHUK
- School of Life SciencesUniversity of DundeeDundee DD1 5EHUK
| | - Dana K. Howe
- Department of Integrative BiologyOregon State UniversityCorvallisOR 97331USA
| | - Inga Zasada
- Horticultural Crops Research LaboratoryU.S. Department of AgricultureCorvallisOR 97330USA
| | - Thomas J. Baum
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | - Jonathan D. Eisenback
- Department of Plant Pathology, Physiology, and Weed ScienceVirginia TechBlacksburgVA 24061USA
| | - Kathryn Kamo
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of AgricultureBeltsvilleMD 20705‐2350USA
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12
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Xiang Y, Wang DW, Li JY, Xie H, Xu CL, Li Y. Transcriptome Analysis of the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi (Aphelenchida: Aphelenchoididae). PLoS One 2016; 11:e0166877. [PMID: 27875578 PMCID: PMC5119785 DOI: 10.1371/journal.pone.0166877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/04/2016] [Indexed: 01/21/2023] Open
Abstract
The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a plant parasitic nematode that attacks many plants. In this study, a transcriptomes of mixed-stage population of CFN was sequenced on the Illumina HiSeq 2000 platform. 68.10 million Illumina high quality paired end reads were obtained which generated 26,817 transcripts with a mean length of 1,032 bp and an N50 of 1,672 bp, of which 16,467 transcripts were annotated against six databases. In total, 20,311 coding region sequences (CDS), 495 simple sequence repeats (SSRs) and 8,353 single-nucleotide polymorphisms (SNPs) were predicted, respectively. The CFN with the most shared sequences was B. xylophilus with 16,846 (62.82%) common transcripts and 10,543 (39.31%) CFN transcripts matched sequences of all of four plant parasitic nematodes compared. A total of 111 CFN transcripts were predicted as homologues of 7 types of carbohydrate-active enzymes (CAZymes) with plant/fungal cell wall-degrading activities, fewer transcripts were predicted as homologues of plant cell wall-degrading enzymes than fungal cell wall-degrading enzymes. The phylogenetic analysis of GH5, GH16, GH43 and GH45 proteins between CFN and other organisms showed CFN and other nematodes have a closer phylogenetic relationship. In the CFN transcriptome, sixteen types of genes orthologues with seven classes of protein families involved in the RNAi pathway in C. elegans were predicted. This research provides comprehensive gene expression information at the transcriptional level, which will facilitate the elucidation of the molecular mechanisms of CFN and the distribution of gene functions at the macro level, potentially revealing improved methods for controlling CFN.
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Affiliation(s)
- Yu Xiang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Dong-Wei Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Jun-Yi Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
- * E-mail:
| | - Chun-Ling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Yu Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
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Phillips WS, Brown AMV, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 2016; 17:706. [PMID: 27595608 PMCID: PMC5011991 DOI: 10.1186/s12864-016-3047-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/27/2016] [Indexed: 01/21/2023] Open
Abstract
Background The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to this conserved structure, such as the division of the genome into multiple chromosomes, have been reported in a diverse set of metazoans. We report on the two circle multipartite mt genome of a newly described cyst nematode, Globodera ellingtonae. Results The G. ellingtonae mt genome was found to be comprised of two circles, each larger than any other multipartite circular mt chromosome yet reported, and both were larger than the single mt circle of the model nematode Caenorhabditis elegans. The genetic content of the genome was disproportionately divided between the two circles, although they shared a ~6.5 kb non-coding region. The 17.8 kb circle (mtDNA-I) contained ten protein-coding genes and two tRNA genes, whereas the 14.4 kb circle (mtDNA-II) contained two protein-coding genes, 20 tRNA genes and both rRNA genes. Perhaps correlated with this division of genetic content, the copy number of mtDNA-II was more than four-fold that of mtDNA-I in individual nematodes. The difference in copy number increased between second-stage and fourth-stage juveniles. Conclusions The segregation of gene types to different mt circles in G. ellingtonae could provide benefit by localizing gene functional types to independent transcriptional units. This is the first report of both two-circle and several-circle mt genomes within a single genus. The differential copy number associated with this multipartite mt organization could provide a model system for deconstructing mechanisms regulating mtDNA copy number both in somatic cells and during germline development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3047-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wendy S Phillips
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA.
| | - Amanda M V Brown
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Amy B Peetz
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| | - Vivian C Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, UK
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Inga A Zasada
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
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Li X, Yang D, Niu J, Zhao J, Jian H. De Novo Analysis of the Transcriptome of Meloidogyne enterolobii to Uncover Potential Target Genes for Biological Control. Int J Mol Sci 2016; 17:E1442. [PMID: 27598122 PMCID: PMC5037721 DOI: 10.3390/ijms17091442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/03/2022] Open
Abstract
Meloidogyne enterolobii is one of the obligate biotrophic root-knot nematodes that has the ability to reproduce on many economically-important crops. We carried out de novo sequencing of the transcriptome of M. enterolobii using Roche GS FLX and obtained 408,663 good quality reads that were assembled into 8193 contigs and 31,860 singletons. We compared the transcripts in different nematodes that were potential targets for biological control. These included the transcripts that putatively coded for CAZymes, kinases, neuropeptide genes and secretory proteins and those that were involved in the RNAi pathway and immune signaling. Typically, 75 non-membrane secretory proteins with signal peptides secreted from esophageal gland cells were identified as putative effectors, three of which were preliminarily examined using a PVX (pGR107)-based high-throughput transient plant expression system in Nicotiana benthamiana (N. benthamiana). Results showed that these candidate proteins suppressed the programmed cell death (PCD) triggered by the pro-apoptosis protein BAX, and one protein also caused necrosis, suggesting that they might suppress plant immune responses to promote pathogenicity. In conclusion, the current study provides comprehensive insight into the transcriptome of M. enterolobii for the first time and lays a foundation for further investigation and biological control strategies.
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Affiliation(s)
- Xiangyang Li
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
- Beijing University of Agriculture, Beijing 102206, China.
| | - Dan Yang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
| | - Junhai Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
- Hainan Engineering Technology Research Center for Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China.
| | - Jianlong Zhao
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
| | - Heng Jian
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
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Fosu-Nyarko J, Jones MGK. Advances in Understanding the Molecular Mechanisms of Root Lesion Nematode Host Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:253-78. [PMID: 27296144 DOI: 10.1146/annurev-phyto-080615-100257] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Root lesion nematodes (RLNs) are one of the most economically important groups of plant nematodes. As migratory endoparasites, their presence in roots is less obvious than infestations of sedentary endoparasites; nevertheless, in many instances, they are the major crop pests. With increasing molecular information on nematode parasitism, available data now reflect the differences and, in particular, similarities in lifestyle between migratory and sedentary endoparasites. Far from being unsophisticated compared with sedentary endoparasites, migratory endoparasites are exquisitely suited to their parasitic lifestyle. What they lack in effectors required for induction of permanent feeding sites, they make up for with their versatile host range and their ability to move and feed from new host roots and survive adverse conditions. In this review, we summarize the current molecular data available for RLNs and highlight differences and similarities in effectors and molecular mechanisms between migratory and sedentary endoparasitic nematodes.
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Affiliation(s)
- John Fosu-Nyarko
- Plant Biotechnology Research Group, School of Veterinary and Life Sciences, Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia 6150, Australia; ,
| | - Michael G K Jones
- Plant Biotechnology Research Group, School of Veterinary and Life Sciences, Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia 6150, Australia; ,
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16
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Espada M, Jones JT, Mota M. Characterization of glutathione S-transferases from the pine wood nematode, Bursaphelenchus xylophilus. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002985] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have previously identified two secreted glutathione S-transferases (GST) expressed in the pharyngeal gland cell of Bursaphelenchus xylophilus, which are upregulated post infection of the host. This study examines the functional role of GSTs in B. xylophilus biology. We analysed the expression profiles of all predicted GSTs in the genome and the results showed that they belong to kappa and cytosolic subfamilies and the majority are upregulated post infection of the host. A small percentage is potentially secreted and none is downregulated post infection of the host. One secreted protein was confirmed as a functional GST and is within a cluster that showed the highest expression fold change in infection. This enzyme has a protective activity that may involve host defences, namely in the presence of terpenoid compounds and peroxide products. These results suggest that GSTs secreted into the host participate in the detoxification of host-derived defence compounds and enable successful parasitism.
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Affiliation(s)
- Margarida Espada
- NemaLab/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
- Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - John T. Jones
- Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9TZ, UK
| | - Manuel Mota
- NemaLab/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
- Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, EPCV, C. Grande 376, 1749-024 Lisbon, Portugal
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17
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Mei Y, Thorpe P, Guzha A, Haegeman A, Blok VC, MacKenzie K, Gheysen G, Jones JT, Mantelin S. Only a small subset of the SPRY domain gene family in Globodera pallida is likely to encode effectors, two of which suppress host defences induced by the potato resistance gene Gpa2. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002875] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Analysis of the genome sequence of the potato cyst nematode, Globodera pallida, has shown that a substantial gene family (approximately 300 sequences) of proteins containing a SPRY domain is present in this species. This is a huge expansion of the gene family as compared to other organisms, including other plant-parasitic nematodes. Some SPRY domain proteins from G. pallida and G. rostochiensis have signal peptides for secretion and are deployed as effectors. One of these SPRYSEC proteins has been shown to suppress host defence responses. We describe further analysis of this gene family in G. pallida. We show that only a minority (10%) of the SPRY domain proteins in this species have a predicted signal peptide for secretion and that the presence of a signal peptide is strongly correlated with the corresponding gene being expressed at the early stages of parasitism. The data suggest that while the gene family is greatly expanded, only a minority of SPRY domain proteins in G. pallida are SPRYSEC candidate effectors. We show that several new SPRYSECs from G. pallida are expressed in the dorsal gland cell and demonstrate that some, but not all, of the SPRYSECs can suppress the hypersensitive response induced by co-expression of the resistance gene Gpa2 and its cognate avirulence factor RBP-1 in Nicotiana benthamiana.
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Affiliation(s)
- Yuanyuan Mei
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Peter Thorpe
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Athanas Guzha
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Annelies Haegeman
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Caritasstraat 21, B-9090 Melle, Belgium
| | - Vivian C. Blok
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland (BIOSS), The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - John T. Jones
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Biology Department, Ghent University, KL Ledeganckstraat, 9000 Ghent, Belgium
| | - Sophie Mantelin
- Dundee Effector Consortium, Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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18
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Voronin D, Abeykoon AMLL, Gunawardene YIS, Dassanayake RS. Absence of Wolbachia endobacteria in Sri Lankan isolates of the nematode parasite of animals Setaria digitata. Vet Parasitol 2014; 207:350-4. [PMID: 25579393 DOI: 10.1016/j.vetpar.2014.12.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/16/2023]
Abstract
Setaria digitata is an animal filarial parasite with natural hosts of cattle and buffaloes that causes mild disease conditions. Infection of non-permissive hosts such as goats, sheep and horses, by this nematode can cause cerebrospinal nematodiasis that leads to lumbar paralysis and the eventual death of the animals and inflicts considerable economic losses on livestock farmers. Wolbachia are obligate mutualistic endosymbionts for some filarial nematodes and are currently being targeted for the control of diseases caused by these parasites. However, little is known about the occurrence of this endosymbiont in the Setariidae family. In this work, worms collected from infected cattle in Sri Lanka were morphologically identified as S. digitata and tested for the presence of Wolbachia by PCR screening using the WSP- and Wolbachia-specific 16S rRNA and multilocus sequence typing primers that were designed to amplify the gatB, coxA, hcpA, ftsZ and fbpA sequences of Wolbachia. The presence of endobacteria in S. digitata was also examined by whole-mount immunofluorescence staining of the parasites and transmission electron microscopic studies. These analyses did not produce evidence of presence of Wolbachia or any other endosymbiotic bacteria in S. digitata, whereas such evidence was found in Brugia malayi, which was used as a positive control in this study.
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Affiliation(s)
- Denis Voronin
- Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, UK; Molecular Parasitology, Lindsley F Kimball Research Institute, New York Blood Center, USA.
| | - A M L L Abeykoon
- Department of Chemistry, Faculty of Science, University of Colombo, Sri Lanka
| | - Y I Silva Gunawardene
- Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Ranil S Dassanayake
- Department of Chemistry, Faculty of Science, University of Colombo, Sri Lanka.
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19
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Eves-van den Akker S, Lilley CJ, Jones JT, Urwin PE. Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes. PLoS Pathog 2014; 10:e1004391. [PMID: 25255291 PMCID: PMC4177990 DOI: 10.1371/journal.ppat.1004391] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/11/2014] [Indexed: 11/18/2022] Open
Abstract
Sedentary endoparasitic nematodes are obligate biotrophs that modify host root tissues, using a suite of effector proteins to create and maintain a feeding site that is their sole source of nutrition. Using assumptions about the characteristics of genes involved in plant-nematode biotrophic interactions to inform the identification strategy, we provide a description and characterisation of a novel group of hyper-variable extracellular effectors termed HYP, from the potato cyst nematode Globodera pallida. HYP effectors comprise a large gene family, with a modular structure, and have unparalleled diversity between individuals of the same population: no two nematodes tested had the same genetic complement of HYP effectors. Individuals vary in the number, size, and type of effector subfamilies. HYP effectors are expressed throughout the biotrophic stages in large secretory cells associated with the amphids of parasitic stage nematodes as confirmed by in situ hybridisation. The encoded proteins are secreted into the host roots where they are detectable by immunochemistry in the apoplasm, between the anterior end of the nematode and the feeding site. We have identified HYP effectors in three genera of plant parasitic nematodes capable of infecting a broad range of mono- and dicotyledon crop species. In planta RNAi targeted to all members of the effector family causes a reduction in successful parasitism. Sedentary plant parasitic nematodes are pathogens that invade plant roots and establish a feeding site. The feeding site is a specialist structure used by the nematode to support its development within the plant. The nematode secretes a suite of proteins, termed ‘effector proteins’ that are responsible for initiating and maintaining the feeding site. The nematode must also evade recognition by the plant defence systems throughout its lifecycle that can last for many weeks. We describe a diverse and variable effector gene family (HYP), the products of which are secreted into the plant by the nematode and are required for successful infection. The variability and modular structure of this gene family can lead to the production of a large array of effector proteins. This diversity may allow the nematodes to combat any resistance mechanisms developed by the plant. Each nematode tested within a population is genetically unique in terms of these effector genes. We found huge variation in the number, size and type of HYP effectors at the level of the individual. This may explain some of the difficulties in breeding nematode resistant plants and has profound implications for those working with other plant pathogens.
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Affiliation(s)
- Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | | | - John T. Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Peter E. Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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20
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Abstract
Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.
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21
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Bauters L, Haegeman A, Kyndt T, Gheysen G. Analysis of the transcriptome of Hirschmanniella oryzae to explore potential survival strategies and host-nematode interactions. MOLECULAR PLANT PATHOLOGY 2014; 15:352-63. [PMID: 24279397 PMCID: PMC6638887 DOI: 10.1111/mpp.12098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The rice root nematode Hirschmanniella oryzae is the most abundant plant-parasitic nematode in flooded rice fields and is distributed world-wide. Although it is economically less important than sedentary nematodes, it can cause severe yield reductions and economic losses in specific environmental conditions. No transcriptome data for this genus were available until now. We have performed 454 sequencing on a mixed life stages population to gain an insight into nematode-plant interactions and nematode survival strategies. The results of two assembly strategies were combined to reduce the redundancy of the data, generating a final dataset of 21 360 contigs. The data were screened for putative plant cell wall-modifying proteins, which facilitate nematode migration through host roots. A β-mannanase, previously not reported in nematodes, was detected in the dataset. The data were screened for putative effector proteins that may alter the host defence mechanism. Two enzymes, chorismate mutase and isochorismatase, thought to be involved in the salicyclic acid pathway, were identified. Experimental treatments of H. oryzae with artificial seawater showed that late embryogenesis abundant (LEA) proteins and SXP/RAL-2 are induced, suggesting that these proteins are involved in the process of anhydrobiosis. The newly generated data can highlight potential differences between sedentary and migratory nematodes, and will be useful in the further study of host-nematode interactions and the developmental biology of this nematode.
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Affiliation(s)
- Lander Bauters
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
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22
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Koshel EI, Aleshin VV, Eroshenko GA, Kutyrev VV. Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague. BIOMED RESEARCH INTERNATIONAL 2014; 2014:135218. [PMID: 24804197 PMCID: PMC3996313 DOI: 10.1155/2014/135218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/05/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.
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Affiliation(s)
- E. I. Koshel
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Aleshin
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- National Research Institute of Physiology, Biochemistry, and Nutrition of Farm Animals, Russian Academy of Agricultural Sciences, Kaluga Region, Borovsk 249013, Russia
| | - G. A. Eroshenko
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Kutyrev
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
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23
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Foster JM, Landmann F, Ford L, Johnston KL, Elsasser SC, Schulte-Hostedde AI, Taylor MJ, Slatko BE. Absence of Wolbachia endobacteria in the human parasitic nematode Dracunculus medinensis and two related Dracunculus species infecting wildlife. Parasit Vectors 2014; 7:140. [PMID: 24685011 PMCID: PMC3994231 DOI: 10.1186/1756-3305-7-140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wolbachia endosymbionts are a proven target for control of human disease caused by filarial nematodes. However, little is known about the occurrence of Wolbachia in taxa closely related to the superfamily Filarioidea. Our study addressed the status of Wolbachia presence in members of the superfamily Dracunculoidea by screening the human parasite Dracunculus medinensis and related species from wildlife for Wolbachia. FINDINGS D. medinensis, D. lutrae and D. insignis specimens were all negative for Wolbachia colonization by PCR screening for the Wolbachia ftsZ, 16S rRNA and Wolbachia surface protein (wsp) sequences. The quality and purity of the DNA preparations was confirmed by amplification of nematode 18S rRNA and cytochrome c oxidase subunit I sequences. Furthermore, Wolbachia endobacteria were not detected by whole mount fluorescence staining, or by immunohistochemistry using a Wolbachia-specific antiserum. In contrast, positive control Brugia malayi worms were shown to harbour Wolbachia by PCR, fluorescence staining and immunohistochemistry. CONCLUSIONS Three examined species of Dracunculus showed no evidence of Wolbachia endobacteria. This supports that members of the superfamily Dracunculoidea are free of Wolbachia. Within the order Spirurida, these endosymbionts appear restricted to the Filarioidea.
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Affiliation(s)
- Jeremy M Foster
- Parasitology Division, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
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Wang F, Li D, Wang Z, Dong A, Liu L, Wang B, Chen Q, Liu X. Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae). PLoS One 2014; 9:e91591. [PMID: 24637831 PMCID: PMC3956754 DOI: 10.1371/journal.pone.0091591] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/13/2014] [Indexed: 01/09/2023] Open
Abstract
Background The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode. Methodology and Principal Findings Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases. Conclusions and Significance The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.
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Affiliation(s)
- Feng Wang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Danlei Li
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
- * E-mail:
| | - Zhiying Wang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Airong Dong
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Lihong Liu
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Buyong Wang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Qiaoli Chen
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xiaohan Liu
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
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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: 805] [Impact Index Per Article: 73.2] [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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Peng H, Gao BL, Kong LA, Yu Q, Huang WK, He XF, Long HB, Peng DL. Exploring the host parasitism of the migratory plant-parasitic nematode Ditylenchus destuctor by expressed sequence tags analysis. PLoS One 2013; 8:e69579. [PMID: 23922743 PMCID: PMC3726699 DOI: 10.1371/journal.pone.0069579] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/10/2013] [Indexed: 11/20/2022] Open
Abstract
The potato rot nematode, Ditylenchus destructor, is a very destructive nematode pest on many agriculturally important crops worldwide, but the molecular characterization of its parasitism of plant has been limited. The effectors involved in nematode parasitism of plant for several sedentary endo-parasitic nematodes such as Heterodera glycines, Globodera rostochiensis and Meloidogyne incognita have been identified and extensively studied over the past two decades. Ditylenchus destructor, as a migratory plant parasitic nematode, has different feeding behavior, life cycle and host response. Comparing the transcriptome and parasitome among different types of plant-parasitic nematodes is the way to understand more fully the parasitic mechanism of plant nematodes. We undertook the approach of sequencing expressed sequence tags (ESTs) derived from a mixed stage cDNA library of D. destructor. This is the first study of D. destructor ESTs. A total of 9800 ESTs were grouped into 5008 clusters including 3606 singletons and 1402 multi-member contigs, representing a catalog of D. destructor genes. Implementing a bioinformatics' workflow, we found 1391 clusters have no match in the available gene database; 31 clusters only have similarities to genes identified from D. africanus, the most closely related species to D. destructor; 1991 clusters were annotated using Gene Ontology (GO); 1550 clusters were assigned enzyme commission (EC) numbers; and 1211 clusters were mapped to 181 KEGG biochemical pathways. 22 ESTs had similarities to reported nematode effectors. Interestedly, most of the effectors identified in this study are involved in host cell wall degradation or modification, such as 1,4-beta-glucanse, 1,3-beta-glucanse, pectate lyase, chitinases and expansin, or host defense suppression such as calreticulin, annexin and venom allergen-like protein. This result implies that the migratory plant-parasitic nematode D. destructor secrets similar effectors to those of sedentary plant nematodes. Finally we further characterized the two D. destructor expansin proteins.
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Affiliation(s)
- Huan Peng
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bing-li Gao
- Huzhou Modern Agricultural Biotechnology Innovation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Zhejiang, China
| | - Ling-an Kong
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing Yu
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Wen-kun Huang
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu-feng He
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-bo Long
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Pests Comprehensive Governance for Tropical Crops, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, China
| | - De-liang Peng
- The Key Laboratory for Biology of Insect Pests and Plant Disease, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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27
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Wang LC, Chen KY, Chang SH, Chung LY, Gan RCR, Cheng CJ, Tang P. Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing. Parasitol Res 2013; 112:3193-202. [PMID: 23828188 PMCID: PMC3742962 DOI: 10.1007/s00436-013-3495-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/07/2013] [Indexed: 12/18/2022]
Abstract
Angiostrongylus cantonensis is an important zoonotic nematode. It is the causative agent of eosinophilic meningitis and eosinophilic meningoencephalitis in humans. However, information of this parasite at the genomic level is very limited. In the present study, the transcriptomic profiles of the fifth-stage larvae (L5) of A. cantonensis were investigated by next-generation sequencing (NGS). In the NGS database established from the larvae isolated from the brain of Sprague–Dawley rats, 31,487 unique genes with a mean length of 617 nucleotides were assembled. These genes were found to have a 46.08 % significant similarity to Caenorhabditis elegans by BLASTx. They were then compared with the expressed sequence tags of 18 other nematodes, and significant matches of 36.09–59.12 % were found. Among these genes, 3,338 were found to participate in 124 Kyoto Encyclopedia of Genes and Genomes pathways. These pathways included 1,514 metabolisms, 846 genetic information processing, 358 environmental information processing, 264 cellular processes, and 91 organismal systems. Analysis of 30,816 sequences with the gene ontology database indicated that their annotations included 5,656 biological processes (3,364 cellular processes, 3,061 developmental processes, and 3,191 multicellular organismal processes), 7,218 molecular functions (4,597 binding and 3,084 catalytic activities), and 4,719 cellular components (4,459 cell parts and 4,466 cells). Moreover, stress-related genes (112 heat stress and 33 oxidation stress) and genes for proteases (159) were not uncommon. This study is the first NGS-based study to set up a transcriptomic database of A. cantonensis L5. The results provide new insights into the survival, development, and host–parasite interactions of this blood-feeding nematode.
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Affiliation(s)
- Lian-chen Wang
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan.
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Sun BF, Xiao JH, He SM, Liu L, Murphy RW, Huang DW. Multiple ancient horizontal gene transfers and duplications in lepidopteran species. INSECT MOLECULAR BIOLOGY 2013; 22:72-87. [PMID: 23211014 DOI: 10.1111/imb.12004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Eukaryotic horizontal gene transfer (HGT) events are increasingly being discovered yet few reports have summarized multiple occurrences in a wide range of species. We systematically investigated HGT events in the order Lepidoptera by employing a series of filters. Bombyx mori, Danaus plexippus and Heliconius melpomene had 13, 12 and 12 HGTs, respectively, from bacteria and fungi. These HGTs contributed a total of 64 predicted genes: 22 to B. mori, 22 to D. plexippus and 20 to H. melpomene. Several new genes were generated by post-transfer duplications. Post-transfer duplication of a suite of functional HGTs has rarely been reported in higher organisms. The distributional patterns of paralogues for certain genes differed in the three species, indicating potential independent duplication or loss events. All of these HGTs had homologues expressed in some other lepidopterans, indicating ancient transfer events. Most HGTs were involved in the metabolism of sugar and amino acids. These HGTs appeared to have experienced amelioration, purifying selection and accelerated evolution to adapt to the background genome of the recipient. The discovery of ancient, massive HGTs and duplications in lepidopterans and their adaptive evolution provides further insights into the evolutionary significance of the events from donors to multicellular host recipients.
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Affiliation(s)
- B F Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Yan X, Cheng XY, Wang YS, Luo J, Mao ZC, Ferris VR, Xie BY. Comparative transcriptomics of two pathogenic pinewood nematodes yields insights into parasitic adaptation to life on pine hosts. Gene 2012; 505:81-90. [PMID: 22705985 DOI: 10.1016/j.gene.2012.05.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/03/2012] [Accepted: 05/18/2012] [Indexed: 02/07/2023]
Abstract
Bursaphelenchus xylophilus and Bursaphelenchus mucronatus are migratory endoparasitic nematodes that live in pine trees. To gain insight into their molecular similarities and differences, transcriptomes of the two nematodes were analysed. A total of 23,765 and 21,782 contigs (>300 bp) were obtained from B. xylophilus and B. mucronatus, respectively. More than 80% of the contigs could map to each other's transcriptome reciprocally. A total of 23,467 and 21,370 Open Reading Frames were predicted, respectively. Besides those known parasitism-related proteins, six new venom allergen-like proteins (VAPs) were found, which were not homologous to known VAPs. Enzymes involved in xenobiotic biodegradation were abundant in the two transcriptomes based on KEGG functional annotation. Metabolism of xenobiotics by cytochrome P450 comprised the main detoxification pathways. The mRNA expression levels of detoxification genes in nematodes living in the host were higher than those in nematodes feeding on fungus. However, there were fewer enzymes involved in the α-pinene degradation. Our results indicate that the two pinewood nematodes have evolved similar molecular mechanisms to adapt to life on pine hosts.
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Affiliation(s)
- Xia Yan
- College of Life Sciences, Beijing Normal University, Beijing, China
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30
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Blaxter M, Kumar S, Kaur G, Koutsovoulos G, Elsworth B. Genomics and transcriptomics across the diversity of the Nematoda. Parasite Immunol 2012; 34:108-20. [PMID: 22044053 DOI: 10.1111/j.1365-3024.2011.01342.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The diversity of biology in nematodes is reflected in the diversity of their genomes. Parasitic species in particular have evolved mechanisms to invade and outwit their hosts, and these offer opportunities for the development of control measures. Genomic analyses can reveal the molecular underpinnings of phenotypes such as parasitism and thus, initiate and support research programmes that explore the manipulation of host and parasite physiologies to achieve favourable outcomes. Wide sampling across nematode diversity allows phylogenetically informed formulation of research hypotheses, identification of core features shared by all species or important evolutionary novelties present in isolated clades. Many nematode species have been investigated through the use of the expressed sequence tag approach, which samples from the transcribed genome. Gene catalogues generated in this way can be explored to reveal the patterns of expression associated with parasitism and candidates for testing as drug targets or vaccine components. Analysis environments, such as NEMBASE facilitate exploitation of these data. The development of new high-throughput DNA-sequencing technologies has facilitated transcriptomic and genomic approaches to parasite biology. Whole genome sequencing offers more complete catalogues of genes and assists a systems approach to phenotype dissection. These efforts are being coordinated through the 959 Nematode Genomes initiative.
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Affiliation(s)
- M Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK.
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31
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Haegeman A, Mantelin S, Jones JT, Gheysen G. Functional roles of effectors of plant-parasitic nematodes. Gene 2011; 492:19-31. [PMID: 22062000 DOI: 10.1016/j.gene.2011.10.040] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/12/2011] [Accepted: 10/20/2011] [Indexed: 11/17/2022]
Abstract
Plant pathogens have evolved a variety of different strategies that allow them to successfully infect their hosts. Plant-parasitic nematodes secrete numerous proteins into their hosts. These proteins, called effectors, have various functions in the plant cell. The most studied effectors to date are the plant cell wall degrading enzymes, which have an interesting evolutionary history since they are believed to have been acquired from bacteria or fungi by horizontal gene transfer. Extensive genome, transcriptome and proteome studies have shown that plant-parasitic nematodes secrete many additional effectors. The function of many of these is less clear although during the last decade, several research groups have determined the function of some of these effectors. Even though many effectors remain to be investigated, it has already become clear that they can have very diverse functions. Some are involved in suppression of plant defences, while others can specifically interact with plant signalling or hormone pathways to promote the formation of nematode feeding sites. In this review, the most recent progress in the understanding of the function of plant-parasitic nematode effectors is discussed.
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
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Haegeman A, Joseph S, Gheysen G. Analysis of the transcriptome of the root lesion nematode Pratylenchus coffeae generated by 454 sequencing technology. Mol Biochem Parasitol 2011; 178:7-14. [PMID: 21513748 DOI: 10.1016/j.molbiopara.2011.04.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/30/2011] [Accepted: 04/04/2011] [Indexed: 10/18/2022]
Abstract
To study interactions between plants and plant-parasitic nematodes, several omics studies have nowadays become extremely useful. Since most data available so far is derived from sedentary nematodes, we decided to improve the knowledge on migratory nematodes by studying the transcriptome of the nematode Pratylenchus coffeae through generating expressed sequence tags (ESTs) on a 454 sequencing platform. In this manuscript we present the generation, assembly and annotation of over 325,000 reads from P. coffeae. After assembling these reads, 56,325 contigs and singletons with an average length of 353bp were selected for further analyses. Homology searches revealed that 25% of these sequences had significant matches to the Swiss-prot/trEMBL database and 29% had significant matches in nematode ESTs. Over 10,000 sequences were successfully annotated, corresponding to over 6000 unique Gene Ontology identifiers and 5000 KEGG orthologues. Different approaches led to the identification of different sequences putatively involved in the parasitism process. Several plant cell wall modifying enzymes were identified, including an arabinogalactan galactosidase, so far identified in cyst nematodes only. Additionally, some new putative cell wall modifying enzymes are present belonging to GHF5 and GHF16, although further functional studies are needed to determine the true role of these proteins. Furthermore, a homologue to a chorismate mutase was found, suggesting that this parasitism gene has a wider occurrence in plant-parasitic nematodes than previously assumed. Finally, the dataset was searched for orthologues against the Meloidogyne genomes and genes involved in the RNAi pathway. In conclusion, the generated transcriptome data of P. coffeae will be very useful in the future for several projects: (1) evolutionary studies of specific gene families, such as the plant cell wall modifying enzymes, (2) the identification and functional analysis of candidate effector genes, (3) the development of new control strategies, e.g. by finding new targets for RNAi and (4) the annotation of the upcoming genome sequence.
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Affiliation(s)
- Annelies Haegeman
- Ghent University, Department of Molecular Biotechnology, Ghent, Belgium
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Cantacessi C, Mitreva M, Campbell BE, Hall RS, Young ND, Jex AR, Ranganathan S, Gasser RB. First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2010; 10:1199-207. [PMID: 20692378 PMCID: PMC3666958 DOI: 10.1016/j.meegid.2010.07.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 07/29/2010] [Indexed: 12/22/2022]
Abstract
Trichostrongylus colubriformis (Strongylida), a small intestinal nematode of small ruminants, is a major cause of production and economic losses in many countries. The aims of the present study were to define the transcriptome of the adult stage of T. colubriformis, using 454 sequencing technology and bioinformatic analyses, and to predict the main pathways that key groups of molecules are linked to in this nematode. A total of 21,259 contigs were assembled from the sequence data produced from a normalized cDNA library; 7876 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and encoded, amongst others, proteins with 'transthyretin-like' (8.8%), 'RNA recognition' (8.4%) and 'metridin-like ShK toxin' (7.6%) motifs. Bioinformatic analyses inferred that relatively high proportions of the C. elegans homologues are involved in biological pathways linked to 'peptidases' (4%), 'ribosome' (3.6%) and 'oxidative phosphorylation' (3%). Highly represented were peptides predicted to be associated with the nervous system, digestion of host proteins or inhibition of host proteases. Probabilistic functional gene networking of the complement of C. elegans orthologues (n=2126) assigned significance to particular subsets of molecules, such as protein kinases and serine/threonine phosphatases. The present study represents the first, comprehensive insight into the transcriptome of adult T. colubriformis, which provides a foundation for fundamental studies of the molecular biology and biochemistry of this parasitic nematode as well as prospects for identifying targets for novel nematocides. Future investigations should focus on comparing the transcriptomes of different developmental stages, both genders and various tissues of this parasitic nematode for the prediction of essential genes/gene products that are specific to nematodes.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Makedonka Mitreva
- Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, Forest Park Boulevard, St. Louis, Missouri, USA
| | - Bronwyn E. Campbell
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Ross S. Hall
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Aaron R. Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Robin B. Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
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Slatko BE, Taylor MJ, Foster JM. The Wolbachia endosymbiont as an anti-filarial nematode target. Symbiosis 2010; 51:55-65. [PMID: 20730111 PMCID: PMC2918796 DOI: 10.1007/s13199-010-0067-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 05/13/2010] [Indexed: 01/05/2023]
Abstract
Human disease caused by parasitic filarial nematodes is a major cause of global morbidity. The parasites are transmitted by arthropod intermediate hosts and are responsible for lymphatic filariasis (elephantiasis) or onchocerciasis (river blindness). Within these filarial parasites are intracellular alpha-proteobacteria, Wolbachia, that were first observed almost 30 years ago. The obligate endosymbiont has been recognized as a target for anti-filarial nematode chemotherapy as evidenced by the loss of worm fertility and viability upon antibiotic treatment in an extensive series of human trials. While current treatments with doxycycline and rifampicin are not practical for widespread use due to the length of required treatments and contraindications, anti-Wolbachia targeting nevertheless appears a promising alternative for filariasis control in situations where current programmatic strategies fail or are unable to be delivered and it provides a superior efficacy for individual therapy. The mechanisms that underlie the symbiotic relationship between Wolbachia and its nematode hosts remain elusive. Comparative genomics, bioinfomatic and experimental analyses have identified a number of potential interactions, which may be drug targets. One candidate is de novo heme biosynthesis, due to its absence in the genome sequence of the host nematode, Brugia malayi, but presence in Wolbachia and its potential roles in worm biology. We describe this and several additional candidate targets, as well as our approaches for understanding the nature of the host-symbiont relationship.
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Affiliation(s)
- Barton E. Slatko
- Molecular Parasitology Division, New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Mark J. Taylor
- Filariasis Research Laboratory, Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
| | - Jeremy M. Foster
- Molecular Parasitology Division, New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
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Haegeman A, Elsen A, De Waele D, Gheysen G. Emerging molecular knowledge on Radopholus similis, an important nematode pest of banana. MOLECULAR PLANT PATHOLOGY 2010; 11:315-23. [PMID: 20447280 PMCID: PMC6640332 DOI: 10.1111/j.1364-3703.2010.00614.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
TAXONOMY Superkingdom Eukaryota; Kingdom Metazoa; Phylum Nematoda; Class Chromadorea; Order Rhabditida; Suborder Tylenchina; Infraorder Tylenchomorpha; Superfamily Tylenchoidea; Family Pratylenchidae; Subfamily Radopholinae; Genus Radopholus. PHYSICAL PROPERTIES Microscopic unsegmented worm; migratory endoparasite of plants. Strong sexual dimorphism; reproduction both by amphimixis and self-fertilization. HOSTS Over 250 different plant species, including citrus, black pepper and banana (main host plant). SYMPTOMS Purple to black lesions and extensive cavities in plant roots, leading to reduced uptake of water and nutrients. In banana, this may result in poor vegetative growth, reduced bunch weight and toppling of plants. DISEASE CONTROL Nematicides, alternative cropping systems, nematode-free planting material, some resistant cultivars. AGRONOMIC IMPORTANCE Major problem in banana plantations in tropical regions worldwide.
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium
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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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Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, Chapman S, Cock PJA, Grenier E, Lilley CJ, Phillips MS, Blok VC. Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. MOLECULAR PLANT PATHOLOGY 2009; 10:815-28. [PMID: 19849787 PMCID: PMC6640342 DOI: 10.1111/j.1364-3703.2009.00585.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In this article, we describe the analysis of over 9000 expressed sequence tags (ESTs) from cDNA libraries obtained from various life cycle stages of Globodera pallida. We have identified over 50 G. pallida effectors from this dataset using bioinformatics analysis, by screening clones in order to identify secreted proteins up-regulated after the onset of parasitism and using in situ hybridization to confirm the expression in pharyngeal gland cells. A substantial gene family encoding G. pallida SPRYSEC proteins has been identified. The expression of these genes is restricted to the dorsal pharyngeal gland cell. Different members of the SPRYSEC family of proteins from G. pallida show different subcellular localization patterns in plants, with some localized to the cytoplasm and others to the nucleus and nucleolus. Differences in subcellular localization may reflect diverse functional roles for each individual protein or, more likely, variety in the compartmentalization of plant proteins targeted by the nematode. Our data are therefore consistent with the suggestion that the SPRYSEC proteins suppress host defences, as suggested previously, and that they achieve this through interaction with a range of host targets.
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Affiliation(s)
- John T Jones
- Plant Pathology Programme, SCRI, Invergowrie, Dundee DD2 5DA, UK.
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Jacob JEM, Vanholme B, Van Leeuwen T, Gheysen G. A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes 2009; 2:192. [PMID: 19778425 PMCID: PMC2761399 DOI: 10.1186/1756-0500-2-192] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/24/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria (mt) contain their own autonomously replicating DNA, constituted as a small circular genome encoding essential subunits of the respiratory chain. Mt DNA is characterized by a genetic code which differs from the standard one. Interestingly, the mt genome of nematodes share some peculiar features, such as small transfer RNAs, truncated ribosomal RNAs and - in the class of Chromadorean nematodes - unidirectional transcription. FINDINGS We present the complete mt genomic sequence (16,791 bp) of the plant-parasitic nematode Radopholus similis (class Chromadorea). Although it has a gene content similar to most other nematodes, many idiosyncrasies characterize the extremely AT-rich mt genome of R. similis (85.4% AT). The secondary structure of the large (16S) rRNA is further reduced, the gene order is unique, the large non-coding region contains two large repeats, and most interestingly, the UAA codon is reassigned from translation termination to tyrosine. In addition, 7 out of 12 protein-coding genes lack a canonical stop codon and analysis of transcriptional data showed the absence of polyadenylation. Northern blot analysis confirmed that only one strand is transcribed and processed. Furthermore, using nucleotide content bias methods, regions for the origin of replication are suggested. CONCLUSION The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution.
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Affiliation(s)
- Joachim E M Jacob
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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An endosymbiotic bacterium in a plant-parasitic nematode: Member of a new Wolbachia supergroup. Int J Parasitol 2009; 39:1045-54. [DOI: 10.1016/j.ijpara.2009.01.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Haegeman A, Vanholme B, Gheysen G. Characterization of a putative endoxylanase in the migratory plant-parasitic nematode Radopholus similis. MOLECULAR PLANT PATHOLOGY 2009; 10:389-401. [PMID: 19400841 PMCID: PMC6640231 DOI: 10.1111/j.1364-3703.2009.00539.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant-parasitic nematodes have developed an arsenal of enzymes to degrade the rigid plant cell wall. In this article, we report the presence of a putative endoxylanase in the migratory endoparasitic nematode Radopholus similis. This enzyme is thought to facilitate the migration of the nematode, as it breaks down xylan, the major component of hemicellulose. The corresponding gene (Rs-xyl1) was cloned and the sequence revealed three small introns. Interestingly, the position of all three introns was conserved in a putative endoxylanase from Meloidogyne hapla, and the position of one intron was conserved in two endoxylanases from Meloidogyne incognita, which suggests a common ancestral gene. The spatial and temporal expression of the Rs-xyl1 gene was examined by in situ hybridization and semi-quantitative reverse transcriptase-polymerase chain reaction. The putative protein consists of a signal peptide, a catalytic domain and a carbohydrate-binding module (CBM). The catalytic domain showed similarity to both glycosyl hydrolase family 5 (GHF5) and GHF30 enzymes. Using Hidden Markov Model profiles and phylogenetic analysis, we were able to show that Rs-XYL1 and its closest homologues are not members of GHF5, as suggested previously, but rather form a subclass within GHF30. Silencing the putative endoxylanase by double-stranded RNA targeting of the CBM region resulted in an average decrease in infection of 60%, indicating that the gene is important for the nematode to complete its life cycle.
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Affiliation(s)
- Annelies Haegeman
- Faculty of Bioscience Engineering (FBE), Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
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Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: the first transcriptome analysis of an Anguinid nematode. Mol Biochem Parasitol 2009; 167:32-40. [PMID: 19383517 DOI: 10.1016/j.molbiopara.2009.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 04/07/2009] [Accepted: 04/12/2009] [Indexed: 11/20/2022]
Abstract
In this study, 4847 expressed sequenced tags (ESTs) from mixed stages of the migratory plant-parasitic nematode Ditylenchus africanus (peanut pod nematode) were investigated. It is the first molecular survey of a nematode which belongs to the family of the Anguinidae (order Rhabditida, superfamily Sphaerularioidea). The sequences were clustered into 2596 unigenes, of which 43% did not show any homology to known protein, nucleotide, nematode EST or plant-parasitic nematode genome sequences. Gene ontology mapping revealed that most putative proteins are involved in developmental and reproductive processes. In addition unigenes involved in oxidative stress as well as in anhydrobiosis, such as LEA (late embryogenesis abundant protein) and trehalose-6-phosphate synthase were identified. Other tags showed homology to genes previously described as being involved in parasitism (expansin, SEC-2, calreticulin, 14-3-3b and various allergen proteins). In situ hybridization revealed that the expression of a putative expansin and a venom allergen protein was restricted to the gland cell area of the nematode, being in agreement with their presumed role in parasitism. Furthermore, seven putative novel candidate parasitism genes were identified based on the prediction of a signal peptide in the corresponding protein sequence and homologous ESTs exclusively in parasitic nematodes. These genes are interesting for further research and functional characterization. Finally, 34 unigenes were retained as good target candidates for future RNAi experiments, because of their nematode specific nature and observed lethal phenotypes of Caenorhabditis elegans homologs.
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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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Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event. BMC Evol Biol 2008; 8:305. [PMID: 18980666 PMCID: PMC2633302 DOI: 10.1186/1471-2148-8-305] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 11/03/2008] [Indexed: 11/22/2022] Open
Abstract
Background Endo-1,4-beta-glucanases or cellulases from the glycosyl hydrolase family 5 (GHF5) have been found in numerous bacteria and fungi, and recently also in higher eukaryotes, particularly in plant-parasitic nematodes (PPN). The origin of these genes has been attributed to horizontal gene transfer from bacteria, although there still is a lot of uncertainty about the origin and structure of the ancestral GHF5 PPN endoglucanase. It is not clear whether this ancestral endoglucanase consisted of the whole gene cassette, containing a catalytic domain and a carbohydrate-binding module (CBM, type 2 in PPN and bacteria) or only of the catalytic domain while the CBM2 was retrieved by domain shuffling later in evolution. Previous studies on the evolution of these genes have focused primarily on data of sedentary nematodes, while in this study, extra data from migratory nematodes were included. Results Two new endoglucanases from the migratory nematodes Pratylenchus coffeae and Ditylenchus africanus were included in this study. The latter one is the first gene isolated from a PPN of a different superfamily (Sphaerularioidea); all previously known nematode endoglucanases belong to the superfamily Tylenchoidea (order Rhabditida). Phylogenetic analyses were conducted with the PPN GHF5 endoglucanases and homologous endoglucanases from bacterial and other eukaryotic lineages such as beetles, fungi and plants. No statistical incongruence between the phylogenetic trees deduced from the catalytic domain and the CBM2 was found, which could suggest that both domains have evolved together. Furthermore, based on gene structure data, we inferred a model for the evolution of the GHF5 endoglucanase gene structure in plant-parasitic nematodes. Our data confirm a close relationship between Pratylenchus spp. and the root knot nematodes, while some Radopholus similis endoglucanases are more similar to cyst nematode genes. Conclusion We conclude that the ancestral PPN GHF5 endoglucanase gene most probably consisted of the whole gene cassette, i.e. the GHF5 catalytic domain and the CBM2, rather than that it evolved by domain shuffling. Our evolutionary model for the gene structure in PPN GHF5 endoglucanases implies the occurrence of an early duplication event, and more recent gene duplications at genus or species level.
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