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Kitagami Y, Matsuda Y. Effect of ectomycorrhizal fungal species on population growth and food preference of a fungivorous nematode. MYCORRHIZA 2022; 32:95-104. [PMID: 34982216 DOI: 10.1007/s00572-021-01063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Fungivorous nematodes can use ectomycorrhizal (ECM) fungi as food resources in forest soils, and they may establish close predator-prey relationships in forest ecosystems. However, the effect of ECM fungal species on the growth of fungivorous nematodes is poorly studied. To identify fungivorous nematode propagation and preference for ECM fungi, we investigated the in vitro population growth and food attraction of the fungivorous nematode Aphelenchoides sp. on media with four ECM fungal species: Cenococcum geophilum, Pisolithus tinctorius, Rhizopogon roseolus and Suillus granulatus. Individual nematodes were fed on hyphae of all four ECM fungal species grown on modified Melin-Norkrans agar media. Nematode numbers were significantly lower on P. tinctorius than on all other fungal species. The other three species produced similar population growth rates, with S. granulatus producing the greatest number of nematodes at 2, 3 and 4 weeks and C. geophilum and R. roseolus producing the largest number after 8 weeks. In the histogram for nematode length classes, a unimodal pattern was fitted for P. tinctorius and R. roseolus, but a bimodal pattern was fitted for C. geophilum and S. granulatus by the Silverman test. The attraction of nematodes to S. granulatus was significantly higher than that to other ECM fungi. Our findings suggest that the propagation and body size of nematodes are ECM fungal species dependent. Predator-prey relationships between fungivorous nematodes and ECM fungi may accelerate nutrient cycles in forest ecosystems.
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Affiliation(s)
- Yudai Kitagami
- Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan.
| | - Yosuke Matsuda
- Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan
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Chen J, Li Z, Lin B, Liao J, Zhuo K. A Meloidogyne graminicola Pectate Lyase Is Involved in Virulence and Activation of Host Defense Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:651627. [PMID: 33868351 PMCID: PMC8044864 DOI: 10.3389/fpls.2021.651627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 05/27/2023]
Abstract
Plant-parasitic nematodes secrete an array of cell-wall-degrading enzymes to overcome the physical barrier formed by the plant cell wall. Here, we describe a novel pectate lyase gene Mg-PEL1 from M. graminicola. Quantitative real-time PCR assay showed that the highest transcriptional expression level of Mg-PEL1 occurred in pre-parasitic second-stage juveniles, and it was still detected during the early parasitic stage. Using in situ hybridization, we showed that Mg-PEL1 was expressed exclusively within the subventral esophageal gland cells of M. graminicola. The yeast signal sequence trap system revealed that it possessed an N-terminal signal peptide with secretion function. Recombinant Mg-PEL1 exhibited hydrolytic activity toward polygalacturonic acid. Rice plants expressing RNA interference vectors targeting Mg-PEL1 showed an increased resistance to M. graminicola. In addition, using an Agrobacterium-mediated transient expression system and plant immune response assays, we demonstrated that the cell wall localization of Mg-PEL1 was required for the activation of plant defense responses, including programmed plant cell death, reactive oxygen species (ROS) accumulation and expression of defense-related genes. Taken together, our results indicated that Mg-PEL1 could enhance the pathogenicity of M. graminicola and induce plant immune responses during nematode invasion into plants or migration in plants. This provides a new insight into the function of pectate lyases in plants-nematodes interaction.
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Affiliation(s)
- Jiansong Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
| | - Zhiwen Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
| | - Borong Lin
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
| | - Jinling Liao
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Kan Zhuo
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
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Zhang Y, Li S, Li H, Wang R, Zhang KQ, Xu J. Fungi-Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture. J Fungi (Basel) 2020; 6:E206. [PMID: 33020457 PMCID: PMC7711821 DOI: 10.3390/jof6040206] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 01/27/2023] Open
Abstract
Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Shuoshuo Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ruirui Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- School of Life Science, Yunnan University, Kunming 650032, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (Y.Z.); (S.L.); (H.L.); (R.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Fu Z, Agudelo P, Wells CE. Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode ( Aphelenchoides fragariae). J Nematol 2020; 52:1-12. [PMID: 32449331 PMCID: PMC7266049 DOI: 10.21307/jofnem-2020-047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
The foliar nematode (Aphelenchoides fragariae) is a quarantined pest that infects a broad range of herbaceous and woody plants. Previous work has demonstrated its remarkable ability to survive rapid and extreme desiccation, although the specific molecular mechanisms underlying its anhydrobiotic response have not been characterized. The authors used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated nematodes. In total, 2,083 and 953 genes were significantly up- and downregulated, respectively, in desiccated nematodes. Of the 100 annotated genes with the largest positive fold-changes, more than one third encoded putative detoxification-related proteins. Genes encoding enzymes of Phase I and Phase II detoxification systems were among the most strongly upregulated in the transcriptome, including 35 cytochrome p450s, 23 short chain dehydrogenase/reductases, 5 glutathione-S-transferases, and 22 UDP-glucuronosyltransferases. Genes encoding heat shock proteins, unfolded protein response enzymes, and intrinsically disordered proteins were also upregulated. Anhydrobiosis in A. fragariae appears to involve both strategies to minimize protein misfolding and aggregation, and wholesale induction of the cellular detoxification machinery. These processes may be controlled in part through the activity of forkhead transcription factors similar to Caenorhabditis elegans’ daf-16, a number of which were differentially expressed under desiccation.
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Affiliation(s)
- Zhen Fu
- School of Agricultural, Forest, and Environmental Sciences , Clemson University , Clemson, SC, 29634 ; Department of Entomology , Washington State University , Pullman, WA, 99164
| | - Paula Agudelo
- School of Agricultural, Forest, and Environmental Sciences , Clemson University , Clemson, SC, 29634
| | - Christina E Wells
- Department of Biological Sciences , Clemson University , Clemson, SC, 29634
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Kitazume H, Dayi M, Tanaka R, Kikuchi T. Assessment of the behaviour and survival of nematodes under low oxygen concentrations. PLoS One 2018; 13:e0197122. [PMID: 29758056 PMCID: PMC5951539 DOI: 10.1371/journal.pone.0197122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 04/26/2018] [Indexed: 11/18/2022] Open
Abstract
Oxygen is required for the completion of almost all known metazoan lifecycles, but many metazoans harbour abilities to withstand varying degrees and periods of hypoxia. Caenorhabditis elegans, one of the most popular model organism is extensively used as a model for the study of hypoxia and anoxia biology and it has been found that this nematode is capable of tolerance to varying degrees of hypoxia. Considering the extremely high diversity of nematodes, the effects of low oxygen concentration and mechanisms of adaptation to oxygen depletion differ among species. In this study, we used a simple assay to examine anoxia tolerance in four nematode species, including three free-living and one plant parasitic nematode. We found that the plant parasitic nematode Bursaphelenchus xylophilus can survive more than 14 days under anoxic conditions. Comparisons of behaviour during anoxia induction and the repertoire of oxygen sensation genes among the tested species suggested the existence of different oxygen sensation systems between B. xylophilus and C. elegans, which quickly introduce suspended animation in response to oxygen depletion to survive long-term anoxia.
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Affiliation(s)
- Hiromi Kitazume
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mehmet Dayi
- Faculty of Forestry, Duzce University, Konuralp Campus, Duzce, Turkey
| | - Ryusei Tanaka
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- * E-mail:
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6
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Cui JK, Peng H, Qiao F, Wang GF, Huang WK, Wu DQ, Peng D. Characterization of Putative Effectors from the Cereal Cyst Nematode Heterodera avenae. PHYTOPATHOLOGY 2018; 108:264-274. [PMID: 28945520 DOI: 10.1094/phyto-07-17-0226-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant-parasitic nematodes that play an important role in the invasion process. A total of 1,480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.
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Affiliation(s)
- Jiang-Kuan Cui
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Huan Peng
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Fen Qiao
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gao-Feng Wang
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Wen-Kun Huang
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Du-Qing Wu
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Deliang Peng
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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7
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Yang Y, Ye Q, Li K, Li Z, Bo X, Li Z, Xu Y, Wang S, Wang P, Chen H, Wang J. Genomics and Comparative Genomic Analyses Provide Insight into the Taxonomy and Pathogenic Potential of Novel Emmonsia Pathogens. Front Cell Infect Microbiol 2017; 7:105. [PMID: 28409126 PMCID: PMC5374152 DOI: 10.3389/fcimb.2017.00105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/16/2017] [Indexed: 12/14/2022] Open
Abstract
Over the last 50 years, newly described species of Emmonsia-like fungi have been implicated globally as sources of systemic human mycosis (emmonsiosis). Their ability to convert into yeast-like cells capable of replication and extra-pulmonary dissemination during the course of infection differentiates them from classical Emmonsia species. Immunocompromised patients are at highest risk of emmonsiosis and exhibit high mortality rates. In order to investigate the molecular basis for pathogenicity of the newly described Emmonsia species, genomic sequencing and comparative genomic analyses of Emmonsia sp. 5z489, which was isolated from a non-deliberately immunosuppressed diabetic patient in China and represents a novel seventh isolate of Emmonsia-like fungi, was performed. The genome size of 5z489 was 35.5 Mbp in length, which is ~5 Mbp larger than other Emmonsia strains. Further, 9,188 protein genes were predicted in the 5z489 genome and 16% of the assembly was identified as repetitive elements, which is the largest abundance in Emmonsia species. Phylogenetic analyses based on whole genome data classified 5z489 and CAC-2015a, another novel isolate, as members of the genus Emmonsia. Our analyses showed that divergences among Emmonsia occurred much earlier than other genera within the family Ajellomycetaceae, suggesting relatively distant evolutionary relationships among the genus. Through comparisons of Emmonsia species, we discovered significant pathogenicity characteristics within the genus as well as putative virulence factors that may play a role in the infection and pathogenicity of the novel Emmonsia strains. Moreover, our analyses revealed a novel distribution mode of DNA methylation patterns across the genome of 5z489, with >50% of methylated bases located in intergenic regions. These methylation patterns differ considerably from other reported fungi, where most methylation occurs in repetitive loci. It is unclear if this difference is related to physiological adaptations of new Emmonsia, but this question warrants further investigation. Overall, our analyses provide a framework from which to further study the evolutionary dynamics of Emmonsia strains and identity the underlying molecular mechanisms that determine the infectious and pathogenic potency of these fungal pathogens, and also provide insight into potential targets for therapeutic intervention of emmonsiosis and further research.
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Affiliation(s)
- Ying Yang
- Academy of Military Medical SciencesBeijing, China.,Department of Biotechnology, Beijing Institute of Radiation MedicineBeijing, China.,Department of Biological Product Control, National Institutes for Food and Drug ControlBeijing, China
| | - Qiang Ye
- Department of Biological Product Control, National Institutes for Food and Drug ControlBeijing, China.,Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech ProductsBeijing, China
| | - Kang Li
- Department of Biological Product Control, National Institutes for Food and Drug ControlBeijing, China.,Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech ProductsBeijing, China
| | - Zongwei Li
- Center for Hospital Infection Control, Chinese PLA Institute for Disease Control and PreventionBeijing, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation MedicineBeijing, China
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation MedicineBeijing, China
| | - Yingchun Xu
- Division of Medical Microbiology, Peking Union Medical College HospitalBeijing, China
| | - Shengqi Wang
- Department of Biotechnology, Beijing Institute of Radiation MedicineBeijing, China
| | - Peng Wang
- Division of Medical Microbiology, Peking Union Medical College HospitalBeijing, China
| | - Huipeng Chen
- Academy of Military Medical SciencesBeijing, China
| | - Junzhi Wang
- Department of Biological Product Control, National Institutes for Food and Drug ControlBeijing, China
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8
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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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9
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Noon JB, Baum TJ. Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. BMC Evol Biol 2016; 16:74. [PMID: 27068610 PMCID: PMC4828791 DOI: 10.1186/s12862-016-0651-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/05/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. RESULTS Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches. CONCLUSIONS GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.
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Affiliation(s)
- Jason B. Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
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10
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Peng H, Cui J, Long H, Huang W, Kong L, Liu S, He W, Hu X, Peng D. Novel Pectate Lyase Genes of Heterodera glycines Play Key Roles in the Early Stage of Parasitism. PLoS One 2016; 11:e0149959. [PMID: 26930215 PMCID: PMC4773153 DOI: 10.1371/journal.pone.0149959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 11/19/2022] Open
Abstract
Pectate lyases are known to play a key role in pectin degradation by catalyzing the random cleavage of internal polymer linkages (endo-pectinases). In this paper, four novel cDNAs, designated Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7, that encode pectate lyases were cloned and characterized from the soybean cyst nematode, Heterodera glycines. The predicted protein sequences of HG-PEL-3, HG-PEL-4 and HG-PEL-6 differed significantly in both their amino acid sequences and their genomic structures from other pectate lyases of H. glycines (HG-PEL-1, HG-PEL-2 and HG-PEL-7). A phylogenetic study revealed that the pectate lyase proteins of H. glycines are clustered into distinct clades and have distinct numbers and positioning of introns, which suggests that the pectate lyase genes of H. glycines may have evolved from at least two ancestral genes. A Southern blot analysis revealed that multiple Hg-pel-6-like genes were present in the H. glycines genome. In situ hybridization showed that four novel pectate lyases (Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7) were actively transcribed in the subventral esophageal gland cells. A semi-quantitative RT-PCR assay supported the finding that the expression of these genes was strong in the egg, pre-parasitic second-stage juvenile (J2) and early parasitic J2 stages and that it declined in further developmental stages of the nematode. This expression pattern suggests that these proteins play a role in the migratory phase of the nematode life cycle. Knocking down Hg-pel-6 using in vitro RNA interference resulted in a 46.9% reduction of the number of nematodes that invaded the plants and a 61.5% suppression of the development of H. glycines females within roots compared to the GFP-dsRNA control. Plant host-derived RNAi induced the silencing of the Hg-pel-6gene, which significantly reduced the nematode infection levels at 7 Days post inoculation (dpi). Similarly, this procedure reduced the number of female adults at 40 dpi, which suggests the important roles of this gene in the early stages of parasitism. Our combined data suggest that two types of pectate lyases are present in the H. glycines genome and may have different roles during infection.
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Affiliation(s)
- Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangkuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haibo Long
- Key Laboratory of Pests Comprehensive Governance for Tropical crops, Ministry of Agriculture, P. R. China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenting He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianqi Hu
- The National Engineering Research Center of Agri-biodiversity Applied Technologies, Yunnan Agricultural University, Kunming, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Quist CW, Smant G, Helder J. Evolution of plant parasitism in the phylum Nematoda. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:289-310. [PMID: 26047569 DOI: 10.1146/annurev-phyto-080614-120057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Within the species-rich and trophically diverse phylum Nematoda, at least four independent major lineages of plant parasites have evolved, and in at least one of these major lineages plant parasitism arose independently multiple times. Ribosomal DNA data, sequence information from nematode-produced, plant cell wall-modifying enzymes, and the morphology and origin of the style(t), a protrusible piercing device used to penetrate the plant cell wall, all suggest that facultative and obligate plant parasites originate from fungivorous ancestors. Data on the nature and diversification of plant cell wall-modifying enzymes point at multiple horizontal gene transfer events from soil bacteria to bacterivorous nematodes resulting in several distinct lineages of fungal or oomycete-feeding nematodes. Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.
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Affiliation(s)
- Casper W Quist
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands; , ,
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12
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Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A, Kanzaki N, Jones JT, Kikuchi T. Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi. BMC Evol Biol 2014; 14:69. [PMID: 24690293 PMCID: PMC3997829 DOI: 10.1186/1471-2148-14-69] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/17/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquired by plant parasitic nematodes that allow them to digest plant cell walls. Unlike the typical glycoside hydrolase (GH) family 5 cellulase genes which are found in several nematode species from the order Tylenchida, members of the GH45 cellulase have only been identified in a cluster including the families Parasitaphelenchidae (with the pinewood nematode Bursaphelenchus xylophilus) and Aphelenchoididae, and their origins remain unknown. RESULTS In order to investigate the distribution and evolution of GH45 cellulase genes in nematodes and fungi we performed a wide ranging screen for novel putative GH45 sequences. This revealed that the sequences are widespread mainly in Ascomycetous fungi and have so far been found in a single major nematode lineage. Close relationships between the sequences from nematodes and fungi were found through our phylogenetic analyses. An intron position is shared by sequences from Bursaphelenchus nematodes and several Ascomycetous fungal species. CONCLUSIONS The close phylogenetic relationships and conserved gene structure between the sequences from nematodes and fungi strongly supports the hypothesis that nematode GH45 cellulase genes were acquired via HGT from fungi. The rapid duplication and turnover of these genes within Bursaphelenchus genomes demonstrate that useful sequences acquired via HGT can become established in the genomes of recipient organisms and may open novel niches for these organisms to exploit.
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Affiliation(s)
- Juan E Palomares-Rius
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional, Apdo. 4084, 14080 Córdoba, Spain
| | - Yuuri Hirooka
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - Isheng J Tsai
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hayato Masuya
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Akina Hino
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Natsumi Kanzaki
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - John T Jones
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
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13
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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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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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Kanzaki N, Tanaka R, Ikeda H, Taki H, Sugiura S, Matsumoto K. Phylogenetic status of insect parasitism in the subfamily Entaphelenchinae Nickle with description of Peraphelenchus orientalis n. sp. (Tylenchomorpha: Aphelenchoididae). J Parasitol 2013; 99:639-49. [PMID: 23496793 DOI: 10.1645/12-118.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The nematode family Aphelenchoididae is a highly divergent group that contains plant parasites, predators, fungal feeders, and insect parasites. It is taxonomically separated into 7 subfamilies. Although molecular phylogenetic relationships among 6 of the subfamilies have been clarified, the phylogenetic position of the subfamily Entaphelenchinae, which is composed of endoparasites of insects, remains unclear. Here, a new entaphelenchid species, Peraphelenchus orientalis n. sp., was isolated from the body cavities of burying beetles, Nicrophorus quadripunctatus, with a 14% prevalence (5 out of 36). The phylogenetic position of the subfamily within the family Aphelenchoididae was determined using morphological and molecular data for the new species. The rRNA sequences suggested that the new species belongs to Clade 3 of Aphelenchoididae, which mostly consists of predators and insect parasites. Although molecular sequences from other entaphelenchid species were not available, the subfamily appears to be monophyletic. The new species is characterized by the absence of a functional rectum and anus and by the presence of 3 pairs of male genital papillae, a loosely coiled male body, and a W-shaped male spicule. Compared with the original description of Peraphelenchus necrophori, P. orientalis n. sp. has significant typological differences, possibly because of misinterpretations during the original description of P. necrophori. Excluding these questionable characters, i.e., presence-absence of functional rectum and anus and number of male genital papillae, the new species is distinguished from P. necrophori by minor morphological characters and morphometric values.
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Affiliation(s)
- Natsumi Kanzaki
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan.
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Rybarczyk-Mydłowska K, Maboreke HR, van Megen H, van den Elsen S, Mooyman P, Smant G, Bakker J, Helder J. Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes. BMC Evol Biol 2012; 12:221. [PMID: 23171084 PMCID: PMC3575306 DOI: 10.1186/1471-2148-12-221] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. RESULTS Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. CONCLUSIONS All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly by lateral genes transfer. More likely, these genes were passed on by ancestors of a family nowadays known as the Pratylenchidae.
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Affiliation(s)
- Katarzyna Rybarczyk-Mydłowska
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Wu Q, Xu Y. Transcriptome profiling of heat-resistant strain Bacillus licheniformis CGMCC3962 producing Maotai flavor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:2033-2038. [PMID: 22283589 DOI: 10.1021/jf204270h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although Maotai flavor liquor is exclusive due to its soy sauce flavor, knowledge of its key compound and production mechanism is still scarce until now. To gain insight into the production mechanism of soy sauce flavor, a soy sauce flavor producing strain with high efficiency and heat-resistant capability was obtained, and the metabolic mechanism of the strain was investigated with the technique of microarray profiling. Because high temperature was a key factor for soy sauce flavor production, the global gene expression of this heat-resistant strain fermented at 55 °C was analyzed. Except for the responsive increase of heat shock proteins, which maintained cell survival during heat stress, biosynthesis of cysteine was also up-regulated. In addition, some metabolites were significantly increased when cysteine was added to the fermentation medium, such as 2,3-butanediol, 3-hydroxy-2-butanone, and tetramethylpyrazine, which were important flavor compounds in soy sauce flavor liquor and might be related with soy sauce flavor. The results indicated that cysteine might play an important role in the formation of soy sauce flavor compound, and it might act as an indirect precursor or stimulator of soy sauce flavor formation. This was the first use of the microarray profiling tool to investigate the fermentative strains for Chinese traditional liquor, which would allow a deeper insight into the mechanism of the formation of soy sauce flavor compound.
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Affiliation(s)
- Qun Wu
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China 214122
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Tyson T, O'Mahony Zamora G, Wong S, Skelton M, Daly B, Jones JT, Mulvihill ED, Elsworth B, Phillips M, Blaxter M, Burnell AM. A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags. BMC Res Notes 2012; 5:68. [PMID: 22281184 PMCID: PMC3296651 DOI: 10.1186/1756-0500-5-68] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/26/2012] [Indexed: 11/13/2022] Open
Abstract
Background Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. Panagrolaimus superbus is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that P. superbus uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis. Results To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of P. superbus. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at http://www.nematodes.org/nembase4/species_info.php?species=PSC. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from P. superbus. Notable among those is a putative lineage expansion of the lea (late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific sxp/ral-2 family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from Phytophthora infestans. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This P. superbus sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants glutathione peroxidase, dj-1 and 1-Cys peroxiredoxin, an shsp sequence and an lea gene. Conclusions P. superbus appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of lea genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of P. superbus.
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Affiliation(s)
- Trevor Tyson
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland.
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de novo analysis and functional classification of the transcriptome of the root lesion nematode, Pratylenchus thornei, after 454 GS FLX sequencing. Int J Parasitol 2012; 42:225-37. [PMID: 22309969 DOI: 10.1016/j.ijpara.2011.11.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/20/2022]
Abstract
The migratory endoparasitic root lesion nematode Pratylenchus thornei is a major pest of the cereals wheat and barley. In what we believe to be the first global transcriptome analysis for P. thornei, using Roche GS FLX sequencing, 787,275 reads were assembled into 34,312 contigs using two assembly programs, to yield 6,989 contigs common to both. These contigs were annotated, resulting in functional assignments for 3,048. Specific transcripts studied in more detail included carbohydrate active enzymes potentially involved in cell wall degradation, neuropeptides, putative plant nematode parasitism genes, and transcripts that could be secreted by the nematode. Transcripts for cell wall degrading enzymes were similar to bacterial genes, suggesting that they were acquired by horizontal gene transfer. Contigs matching 14 parasitism genes found in sedentary endoparasitic nematodes were identified. These genes are thought to function in suppression of host defenses and in feeding site development, but their function in P. thornei may differ. Comparison of the common contigs from P. thornei with other nematodes showed that 2,039 were common to sequences of the Heteroderidae, 1,947 to the Meloidogynidae, 1,218 to Radopholus similis, 1,209 matched expressed sequence tags (ESTs) of Pratylenchus penetrans and Pratylenchus vulnus, and 2,940 to contigs of Pratylenchus coffeae. There were 2,014 contigs common to Caenarhabditis elegans, with 15.9% being common to all three groups. Twelve percent of contigs with matches to the Heteroderidae and the Meloidogynidae had no homology to any C. elegans protein. Fifty-seven percent of the contigs did not match known sequences and some could be unique to P. thornei. These data provide substantial new information on the transcriptome of P. thornei, those genes common to migratory and sedentary endoparasitic nematodes, and provide additional understanding of genes required for different forms of parasitism. The data can also be used to identify potential genes to study host interactions and for crop protection.
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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, Jones JT, Danchin EGJ. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:879-87. [PMID: 21539433 DOI: 10.1094/mpmi-03-11-0055] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The origin of plant parasitism within the phylum Nematoda is intriguing. The ability to parasitize plants has originated independently at least three times during nematode evolution and, as more molecular data has emerged, it has become clear that multiple instances of horizontal gene transfer (HGT) from bacteria and fungi have played a crucial role in the nematode's adaptation to this new lifestyle. The first reported HGT cases in plant-parasitic nematodes were genes encoding plant cell wall-degrading enzymes. Other putative examples of HGT were subsequently described, including genes that may be involved in the modulation of the plant's defense system, the establishment of a nematode feeding site, and the synthesis or processing of nutrients. Although, in many cases, it is difficult to pinpoint the donor organism, candidate donors are usually soil dwelling and are either plant-pathogenic or plant-associated microorganisms, hence occupying the same ecological niche as the nematodes. The exact mechanisms of transfer are unknown, although close contacts with donor microorganisms, such as symbiotic or trophic interactions, are a possibility. The widespread occurrence of horizontally transferred genes in evolutionarily independent plant-parasitic nematode lineages suggests that HGT may be a prerequisite for successful plant parasitism in nematodes.
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
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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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Gagnière N, Jollivet D, Boutet I, Brélivet Y, Busso D, Da Silva C, Gaill F, Higuet D, Hourdez S, Knoops B, Lallier F, Leize-Wagner E, Mary J, Moras D, Perrodou E, Rees JF, Segurens B, Shillito B, Tanguy A, Thierry JC, Weissenbach J, Wincker P, Zal F, Poch O, Lecompte O. Insights into metazoan evolution from Alvinella pompejana cDNAs. BMC Genomics 2010; 11:634. [PMID: 21080938 PMCID: PMC3018142 DOI: 10.1186/1471-2164-11-634] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 11/16/2010] [Indexed: 11/29/2022] Open
Abstract
Background Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. Results We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity. Conclusions Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.
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Affiliation(s)
- Nicolas Gagnière
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CERBM F-67400 Illkirch, France
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Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci U S A 2010; 107:17651-6. [PMID: 20876108 DOI: 10.1073/pnas.1008486107] [Citation(s) in RCA: 266] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lateral gene transfer from prokaryotes to animals is poorly understood, and the scarce documented examples generally concern genes of uncharacterized role in the receiver organism. In contrast, in plant-parasitic nematodes, several genes, usually not found in animals and similar to bacterial homologs, play essential roles for successful parasitism. Many of these encode plant cell wall-degrading enzymes that constitute an unprecedented arsenal in animals in terms of both abundance and diversity. Here we report that independent lateral gene transfers from different bacteria, followed by gene duplications and early gain of introns, have shaped this repertoire. We also show protein immunolocalization data that suggest additional roles for some of these cell wall-degrading enzymes in the late stages of these parasites' life cycle. Multiple functional acquisitions of exogenous genes that provide selective advantage were probably crucial for the emergence and proficiency of plant parasitism in nematodes.
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