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Čermák V, Nježić B, Nazarashvili N, Gvritishvili E, Tománková K, Orságová H, Majeská M, Foit J, Vieira P. Bursaphelenchus mucronatus (Nematoda: Parasitaphelenchidae) associated with Monochamus galloprovincialis from Bosnia and Herzegovina and Georgia. Helminthologia 2023; 60:227-239. [PMID: 38152471 PMCID: PMC10750248 DOI: 10.2478/helm-2023-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/06/2023] [Indexed: 12/29/2023] Open
Abstract
Bursaphelenchus mucronatus was detected in association with the pine sawyer beetle (Monochamus galloprovincialis) during the implementation and testing of cross traps with insect attractants as an efficient tool for detection survey for pine wood nematode (Bursaphelenchus xylophilus) in Bosnia and Herzegovina and Georgia in 2017 and 2018, respectively. This nematode was characterized by morphological, morphometric and molecular features. This is the first report of B. mucronatus in association with a M. galloprovincialis in Bosnia and Herzegovina and in Georgia.
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Affiliation(s)
- V. Čermák
- Central Institute for Supervising and Testing in Agriculture, Division of Plant Pest Diagnostics, Šlechtitelů 773/23, 779 00Olomouc, Czech Republic
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Zemědělská 3, 613 00Brno, Czech Republic
| | - B. Nježić
- University of Banja Luka, Faculty of Agriculture, Bulevar vojvode Petra Bojovića 1A, 78 000Banja Luka, Bosnia and Herzegovina
| | - N. Nazarashvili
- State Laboratory of Agriculture, Plant Pest Diagnostic Department, 49 Godziashvili street, 0159Tbilisi, Georgia
| | - E. Gvritishvili
- State Laboratory of Agriculture, Plant Pest Diagnostic Department, 49 Godziashvili street, 0159Tbilisi, Georgia
| | - K. Tománková
- Central Institute for Supervising and Testing in Agriculture, Division of Plant Pest Diagnostics, Šlechtitelů 773/23, 779 00Olomouc, Czech Republic
| | - H. Orságová
- Central Institute for Supervising and Testing in Agriculture, Division of Plant Pest Diagnostics, Šlechtitelů 773/23, 779 00Olomouc, Czech Republic
| | - M. Majeská
- Palacký University in Olomouc, Czech Advanced Technology Research Institute, Plant Genetics and Engineering, Šlechtitelů 27, 779 00Olomouc, Czech Republic
| | - J. Foit
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Zemědělská 3, 613 00Brno, Czech Republic
| | - P. Vieira
- United States Department of Agriculture, Agricultural Research Services, Mycology & Nematology Genetic Diversity & Biology Lab, Beltsville, MD20705, USA
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Generation of a novel antibody against BxPrx, a diagnostic marker of pine wilt disease. Mol Biol Rep 2023; 50:4715-4721. [PMID: 36899277 DOI: 10.1007/s11033-023-08342-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND Bursaphelenchus xylophilus is a pathogenic nematode that causes pine wilt disease (PWD). To prevent the rapid spread of this pathogen, developing a method for rapid and accurate detection of B. xylophilus is required. METHODS AND RESULTS In this study, we produced a B. xylophilus peroxiredoxin (BxPrx), which is a protein that is overexpressed in B. xylophilus. Using recombinant BxPrx as an antigen, we generated and selected a novel antibody that binds to BxPrx via phage display and biopanning. We subcloned the anti-BxPrx single-chain variable fragment-encoding phagemid DNA to mammalian expression vector. We transfected the plasmid into mammalian cells and produced a highly sensitive recombinant antibody that enabled nanogram order detection of BxPrx. CONCLUSION The sequence of anti-BxPrx antibody as well as the rapid immunoassay system described here can be applied for rapid and accurate diagnosis of PWD.
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Li M, Li H, Ding X, Wang L, Wang X, Chen F. The Detection of Pine Wilt Disease: A Literature Review. Int J Mol Sci 2022; 23:ijms231810797. [PMID: 36142710 PMCID: PMC9505960 DOI: 10.3390/ijms231810797] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
Pine wilt disease (PWD) is a global quarantine disease of forests that mainly affects Pinaceae species. The disease spreads rapidly. Once infected, pine trees have an extremely high mortality rate. This paper provides a summary of the common techniques used to detect PWD, including morphological-, molecular-, chemical- and physical-based methods. By comprehending the complex relationship among pinewood nematodes, vectors and host pine trees and employing the available approaches for nematode detection, we can improve the implementation of intervention and control measures to effectively reduce the damage caused by PWD. Although conventional techniques allow a reliable diagnosis of the symptomatic phase, the volatile compound detection and remote sensing technology facilitate a rapid diagnosis during asymptomatic stages. Moreover, the remote sensing technology is capable of monitoring PWD over large areas. Therefore, multiple perspective evaluations based on these technologies are crucial for the rapid and effective detection of PWD.
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Shao H, Xue Q, Yao K, Cui J, Huang W, Kong L, Li C, Li H, Peng D, Smiley RW, Peng H. Origin and Phylogeography of Chinese Cereal Cyst Nematode Heterodera avenae Revealed by Mitochondrial COI Sequences. PHYTOPATHOLOGY 2022; 112:1988-1997. [PMID: 35509208 DOI: 10.1094/phyto-12-21-0532-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Heterodera avenae, a globally distributed plant-parasitic nematode, is one of the most significant pests on cereal crops. In China, it is widely distributed in cereal-growing areas of 16 provinces and causes serious yield losses. In the present study, a total of 98 populations of H. avenae were collected from major wheat-growing regions in China and six other countries. The mitochondrial COI genes were amplified and analyzed. Forty-one mitochondrial COI haplotypes were identified, suggesting a high genetic diversity and endemism level of H. avenae in China. Phylogenetic analysis showed that H. avenae populations in China were divided into four clades. Significant evolutionary and genetic differences were found between Chinese (except Hubei) and foreign populations. Hap1, the most widely distributed haplotype, was considered to be a separate evolutionary origin in China. The gene flow of H. avenae from the northwestern region to the north China region and Huang-Huai-Hai region was significant, so as the direction between north China and Huang-Huai-Hai region. We speculate that water flowing from the Yellow River and mechanical harvesters promoted gene exchange among these groups. A distance-based redundancy analysis showed that genetic distances observed among H. avenae populations were explained foremost not only by geographic distance but also by temperature and precipitation. This study provides theoretical support for the origin and spread of H. avenae populations in China and elsewhere in the world.
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Affiliation(s)
- Hudie Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, P. R. China
| | - Qin Xue
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Ke Yao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Jiangkuan Cui
- State Key Laboratory of Wheat and Maize Crop Science/College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Chuanren Li
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, P. R. China
| | - Hongmei Li
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Richard W Smiley
- Columbia Basin Agricultural Research Center, Oregon State University, Pendleton, Oregon, 97801, U.S.A
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
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Molecular Analysis of the Heterakis dispar Population in Domestic Geese Based on the ITS1-5.8rRNA-ITS2 Fragment. Animals (Basel) 2022; 12:ani12070926. [PMID: 35405914 PMCID: PMC8996868 DOI: 10.3390/ani12070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Heterakis is a nematode which infects the ceca of birds. In geese, Heterakis dispar is the most common species. Due to the scarcity of data concerning the H. dispar population, we are providing this analysis based on the ITS1-5.8rRNA-ITS2 region, one of the most frequently used fragments in genetic analysis. We analyzed 71 H. dispar specimens isolated from 20 geese flocks. In the analyzed fragment, four nucleotide differences were noted, resulting in six types of sequences (A, B, C, D, E, and F). The most frequently noted type was type A (45%), followed by type B (18.3%), type C and D (11.3%), type E (8.5%), and finally, type F (5.6%). Infection with nematodes from different types of groups was noted in 30% of flocks, with type A being the most prevalent, followed by types B, D, or E to make up the remaining 100%. This study represents the first H. dispar population analysis based on the ITS1-5.8rRNA-ITS2 fragment. Abstract Heterakidosis is a parasitic infection in birds caused by the cecal parasite Heterakis spp. The most common species in geese is H. dispar, the largest avian heterakids species. Because of a scarcity of data concerning the H. dispar population, the aim of this study was the genetic analysis of Heterakis dispar isolated from geese flocks based on the ITS1-5.8rRNA-ITS2 fragment. Among the 71 H. dispar specimens isolated from 20 geese flocks, six haplotypes were determined (A, B, C, D, E, and F). The four nucleotide substitutions were noted in both ITS fragments, and all of them were transitions between adenine and guanine, or thymine and cytosine. The most frequently noted haplotype was type A (45%), followed by type B (18.3%), type C and D (11.3%), type E (8.5%), and F (5.6%). Infection with nematodes from different haplotype groups was noted in 30% of the flocks, with type A being the most prevalent, followed by types B, D, or E to make up 100%. This study represents the first H. dispar population analysis based on the ITS1-5.8rRNA-ITS2 fragment.
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Oliveira SA, Baeza JA, Agudelo P, DeWalt SJ. Observations on the Population Genetic Structure of the Leaf Galling Nematode, Ditylenchus gallaeformans. PHYTOPATHOLOGY 2022; 112:881-887. [PMID: 34495679 DOI: 10.1094/phyto-04-21-0174-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Ditylenchus gallaeformans is a plant parasitic nematode that induces galls on aboveground parts of Melastomataceae plants. It differs from most gall-inducing nematodes in that it is not an endoparasite and has been considered as a possible biological control agent against invasive species of Miconia. Little is known about D. gallaeformans biology, genetic differences among populations, and host preferences. This study examined the genetic differences among D. gallaeformans populations from different locations and host species and the phylogenetic relationships among them. Nematodes were collected from galls in plants from Costa Rica, Dominica, and Trinidad. The Cytochrome c oxidase 1 (cox1) region was sequenced from a total of 33 individual nematodes isolated from 33 different plant individuals, representing 21 species of Melastomataceae. Phylogenetic reconstructions, haplotype networks, and analysis of molecular variance showed that the species is monophyletic and has three major clades, which were mostly consistent with geographic location but not with host species. The first clade was composed by two subclades, one with individuals from Costa Rica and one with individuals from Dominica. The second and third clades comprised nematodes only from Trinidad. Overall, there is no evidence of host-species specialization in D. gallaeformans. Biocontrol efforts using the nematode against invasive Miconia could focus on geographical location matching but likely will not need to match host species.
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Affiliation(s)
- Samara A Oliveira
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, U.S.A
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL 34949, U.S.A
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Paula Agudelo
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - Saara J DeWalt
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, U.S.A
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Ding X, Guo Y, Ye J, Wu X, Lin S, Chen F, Zhu L, Huang L, Song X, Zhang Y, Dai L, Xi X, Huang J, Wang K, Fan B, Li D. Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data. PEST MANAGEMENT SCIENCE 2022; 78:1213-1226. [PMID: 34839581 PMCID: PMC9300093 DOI: 10.1002/ps.6738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/09/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Bursaphelenchus xylophilus, the pinewood nematode, kills millions of pine trees worldwide every year, and causes enormous economic and ecological losses. Despite extensive research on population variation, there is little understanding of the population-wide variation spectrum in China. RESULTS We sequenced an inbred B. xylophilus strain using Pacbio+Illumina+Bionano+Hi-C and generated a chromosome-level assembly (AH1) with six chromosomes of 77.1 Mb (chromosome N50: 12 Mb). The AH1 assembly shows very high continuity and completeness, and contains novel genes with potentially important functions compared with previous assemblies. Subsequently, we sequenced 181 strains from China and the USA and found ~7.8 million single nucleotide polymorphisms (SNPs). Analysis shows that the B. xylophilus population in China can be divided into geographically bounded subpopulations with severe cross-infection and potential migrations. In addition, distribution of B. xylophilus is dominated by temperature zones while geographically associated SNPs are mainly located on adaptation related GPCR gene families, suggesting the nematode has been evolving to adapt to different temperatures. A machine-learning based epidemic tracking method has been established to predict their geographical origins, which can be applied to any other species. CONCLUSION Our study provides the community with the first high-quality chromosome-level assembly which includes a comprehensive catalogue of genetic variations. It provides insights into population structure and effective tracking method for this invasive species, which facilitates future studies to address a variety of applied, genomic and evolutionary questions in B. xylophilus as well as related species.
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Affiliation(s)
- Xiaolei Ding
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
| | - Yunfei Guo
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Jianren Ye
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaoqin Wu
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Sixi Lin
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Fengmao Chen
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Lihua Zhu
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Lin Huang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaofeng Song
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjingChina
| | - Yi Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Ling Dai
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaotong Xi
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Jinsi Huang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Ben Fan
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - De‐Wei Li
- The Connecticut Agricultural Experiment Station Valley LaboratoryWindsorCTUSA
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Guil N, Guidetti R, Cesari M, Marchioro T, Rebecchi L, Machordom A. Molecular Phylogenetics, Speciation, and Long Distance Dispersal in Tardigrade Evolution: A case study of the genusMilnesium. Mol Phylogenet Evol 2022; 169:107401. [PMID: 35031462 DOI: 10.1016/j.ympev.2022.107401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
Microorganisms (sensu lato, i.e., including micrometazoans) are thought to have cosmopolitan geographic distributions due to their theoretically unlimited dispersal capabilities, a consequence of their tiny size, population dynamics, and resistant forms. However, several molecular studies of microorganisms have identified biogeographic patterns indicating cryptic speciation and/or weak species definitions. Using a multi-locus approach with the genus Milnesium (Tardigrada), we aimed to determine the genetic structure of populations worldwide and the effects of long distance dispersal (LDD) on genetic connectivity and relationships across the six continents. Our results on this micrometazoan's genetic structure and LDD at global and micro-local scales indicate contrasting patterns not easily explained by a unique or simple phenomenon. Overall, we report three key findings: (i) confirmation of long distance dispersal for tardigrades, (ii) populations with globally-shared or endemic micro-local haplotypes, and (iii) a supported genetic structure instead of the homogeneous genetic distribution hypothesized for microorganisms with LDD capabilities. Moreover, incongruences between our morphological and molecular results suggest that species delimitation within the genus Milnesium could be problematic due to homoplasy. Duality found for Milnesium populations at the global scale, namely, a molecular phylogenetic structure mixed with widely distributed haplotypes (but without any apparent biogeographic structure), is similar to patterns observed for some unicellular, prokaryotic and eukaryotic, microorganisms. Factors influencing these patterns are discussed within an evolutionary framework.
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Affiliation(s)
- N Guil
- Department of Biodiversity and Evolutionary Biology. Museo Nacional de Ciencias Naturales (MNCN-CSIC). José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
| | - R Guidetti
- Department of Life Sciences. University of Modena and Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - M Cesari
- Department of Life Sciences. University of Modena and Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - T Marchioro
- Department of Life Sciences. University of Modena and Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - L Rebecchi
- Department of Life Sciences. University of Modena and Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - A Machordom
- Department of Biodiversity and Evolutionary Biology. Museo Nacional de Ciencias Naturales (MNCN-CSIC). José Gutiérrez Abascal, 2, 28006, Madrid, Spain
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Copy Number Variations of Glycoside Hydrolase 45 Genes in Bursaphelenchus xylophilus and Their Impact on the Pathogenesis of Pine Wilt Disease. FORESTS 2021. [DOI: 10.3390/f12030275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The pine wood nematode Bursaphelenchus xylophilus parasitizes millions of pine trees worldwide each year, causing severe wilt and the death of host trees. Glycoside hydrolase 45 genes of B. xylophilus are reported to have been acquired by horizontal gene transfer from fungi and are responsible for cell wall degradation during nematode infection. Previous studies ignored the possibility of copy number variations of such genes. In this study, we determined that two of the glycoside hydrolase 45 genes evolved to maintain multiple copies with distinct expression levels, enabling the nematode to infect a variety of pine hosts. Additionally, tandem repeat variations within coding regions were also detected between different copies of glycoside hydrolase 45 genes that could result in changes in protein sequences and serve as an effective biological marker to detect copy number variations among different B. xylophilus populations. Consequently, we were able to further identify the copy number variations of glycoside hydrolase 45 genes among B. xylophilus strains with different virulence. Our results provide new insights into the pathogenicity of B. xylophilus, provide a practical marker to genotype copy number variations and may aid in population classification.
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Maehara N, Kanzaki N, Aikawa T, Nakamura K. Potential vector switching in the evolution of Bursaphelenchus xylophilus group nematodes (Nematoda: Aphelenchoididae). Ecol Evol 2020; 10:14320-14329. [PMID: 33391718 PMCID: PMC7771127 DOI: 10.1002/ece3.7033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/12/2020] [Accepted: 10/21/2020] [Indexed: 12/02/2022] Open
Abstract
To show the importance of vector switching of nematodes in the evolution of the Bursaphelenchus xylophilus group, we tested a hypothesis that "Bursaphelenchus doui (or its ancestor) was transferred by Acalolepta fraudatrix, Acalolepta sejuncta, and/or Monochamus subfasciatus (or their ancestral species) from broad-leaved trees to conifers, switched vectors from these cerambycid beetles to Monochamus beetles in conifers, and then evolved into the common ancestor of Bursaphelenchus mucronatus and B. xylophilus." We used a simple nematode-loading method to beetles and produced 20 binary combinations of five B. xylophilus group species and four cerambycid beetle species in the tribe Lamiini. The affinity of the nematodes for the beetles was examined based on phoretic stage formation of the nematodes. Phoretic stages of B. doui appeared in all beetle species examined, namely Acalolepta luxuriosa, Psacothea hilaris, A. fraudatrix, and Monochamus alternatus, although the affinity of the nematode for M. alternatus was weak. This finding indicates that B. doui could switch vectors to conifer-using Monochamus beetles after transfer by A. fraudatrix from broad-leaved trees to conifers. We conclude that vector switching of nematodes could have potentially happened during the evolutionary history of the B. xylophilus group.
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Affiliation(s)
- Noritoshi Maehara
- Department of Forest EntomologyForestry and Forest Products Research InstituteTsukubaJapan
| | - Natsumi Kanzaki
- Kansai Research CenterForestry and Forest Products Research InstituteKyotoJapan
| | - Takuya Aikawa
- Tohoku Research CenterForestry and Forest Products Research InstituteMoriokaJapan
| | - Katsunori Nakamura
- Tohoku Research CenterForestry and Forest Products Research InstituteMoriokaJapan
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Molecular variation among virulent and avirulent strains of the quarantine nematode Bursaphelenchus xylophilus. Mol Genet Genomics 2020; 296:259-269. [PMID: 33169231 PMCID: PMC7895788 DOI: 10.1007/s00438-020-01739-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023]
Abstract
Bursaphelenchus xylophilus is an emerging pathogenic nematode that is responsible for a devastating epidemic of pine wilt disease worldwide, causing severe ecological damage and economic losses to forestry. Two forms of this nematode have been reported, i.e., with strong and weak virulence, commonly referred as virulent and avirulent strains. However, the pathogenicity-related genes of B. xylophilus are not sufficiently characterized. In this study, to find pathogenesis related genes we re-sequenced and compared genomes of two virulent and two avirulent populations. We identified genes affected by genomic variation, and functional annotation of those genes indicated that some of them might play potential roles in pathogenesis. The performed analysis showed that both avirulent populations differed from the virulent ones by 1576 genes with high impact variants. Demonstration of genetic differences between virulent and avirulent strains will provide effective methods to distinguish these two nematode virulence forms at the molecular level. The reported results provide basic information that can facilitate development of a better diagnosis for B. xylophilus isolates/strains which present different levels of virulence and better understanding of the molecular mechanism involved in the development of the PWD.
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Investigation of Pinewood Nematodes in Pinus tabuliformis Carr. under Low-Temperature Conditions in Fushun, China. FORESTS 2020. [DOI: 10.3390/f11090993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In recent years, the pinewood nematode has continuously adapted to low-temperature environments and expanded from the South to the North of China. In December 2018, a large area of pinewood nematode was suspected to be harmful to Pinus tabuliformis under natural conditions in Fushun City, Liaoning Province. In order to clarify the low-temperature environment and population characteristics of pinewood nematodes in this new epidemic area, we analyzed the difference in temperature between the inside and outside of P. tabuliformis in low-temperature environments, conducted the morphological and molecular identification of pinewood nematodes in P. tabuliformis, summarized the distribution characteristics of the wintering of pinewood nematodes and explored the population structure of pinewood nematodes under different low-temperature conditions. The results indicated that the diurnal variation of temperature in dead P. tabuliformis was significantly less than the environment temperature. The lowest temperature in P. tabuliformis was 3.2 °C higher than the lowest temperature in the environment in one day; the pathogen of a large area of dead P. tabuliformis in Fushun was pinewood nematode (Bursaphelenchus xylophilus); 84.9% of the average populations of pinewood nematodes were third-stage dispersal juveniles, which mainly gathered in 5 cm within the pupal chamber of Monochamus saltuarius Gebler. At −40 ℃, most of the third-stage dispersal juveniles of pinewood nematode in dead pine can still survive. Our study laid a foundation for the understanding of the low-temperature adaptation mechanism of pinewood nematode and contributed to the monitoring of pine wilt disease in the mid-temperate zone.
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Wu S, Gao S, Wang S, Meng J, Wickham J, Luo S, Tan X, Yu H, Xiang Y, Hu S, Zhao L, Sun J. A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. Genes (Basel) 2020; 11:genes11050570. [PMID: 32438771 PMCID: PMC7288286 DOI: 10.3390/genes11050570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the invasive B. xylophilus has been published, the absence of a reference genome of B. mucronatus still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of B. mucronatus, including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between B. xylophilus and B. mucronatus. However, the losing of orphan genes and species-specific orthologous genes in B. mucronatus may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in B. mucronatus may jointly contribute to its displacement by B. xylophilus. Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of B. mucronatus, especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases.
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Affiliation(s)
- Shuangyang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Sen Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Jie Meng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob Wickham
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
| | - Yujia Xiang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (S.G.); (S.W.); (S.L.); (X.T.); (H.Y.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (S.W.); (J.M.); (J.W.); (Y.X.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-64807121
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Liu Z, Li Y, Pan L, Meng F, Zhang X. Cold adaptive potential of pine wood nematodes overwintering in plant hosts. Biol Open 2019; 8:bio.041616. [PMID: 31023716 PMCID: PMC6550080 DOI: 10.1242/bio.041616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The pine wood nematode (PWN; Bursaphelenchus xylophilus) is the causal agent of pine wilt disease, which results in severe ecological and economic losses in coniferous forests. During overwintering, PWNs undergo morphological and physiological changes to adapt to low temperature environments. Here, the physiological changes of the PWN populations sampled in the summer and winter were compared to analyze the role of low temperatures in their response. The PWN overwinters as third-stage dispersal juveniles, which showed significantly greater survival rates than summer populations (propagative forms) at sub-zero temperatures. The major biochemical compounds in the populations were analyzed by gas chromatography. Eight dominant fatty acids, with stearic acid being the most important, were identified from PWN propagative stage and third-stage dispersal stage. Compared with the propagative stage, the dispersal stage showed significant increases in the fatty acid content and the proportion of unsaturated fatty acids. Three carbohydrates, trehalose, glycerol and glucose, were detected in the PWN. Compared with the summer population, the levels of trehalose and glycerol increased significantly, while glucose decreased, in the winter population. The modifications in fatty acid composition and cryoprotectant levels, as elements of its changing physiology, play important roles in the overwintering success of the PWN. Summary: The modifications in fatty acid composition and cryoprotectant levels, as elements of its changing physiology, play important roles in the overwintering success of the pine wood nematode.
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Affiliation(s)
- Zhenkai Liu
- Laboratory of Forestry Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing Jiangsu, 210037, People's Republic of China
| | - Yongxia Li
- Laboratory of Forestry Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing Jiangsu, 210037, People's Republic of China
| | - Long Pan
- Laboratory of Forestry Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing Jiangsu, 210037, People's Republic of China
| | - Fanli Meng
- Laboratory of Forestry Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing Jiangsu, 210037, People's Republic of China
| | - Xingyao Zhang
- Laboratory of Forestry Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing Jiangsu, 210037, People's Republic of China
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Liu C, Hu Z, Wang X, Geng Y, Ma C, Wang Z, Li R, Shi C. Rapid Detection of the Bursaphelenchus Xylophilus by Denaturation Bubble-mediated Strand Exchange Amplification. ANAL SCI 2019; 35:449-453. [PMID: 30606901 DOI: 10.2116/analsci.18p461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bursaphelenchus xylophilus (B. xylophilus) is one of the most important causal agents of infectious diseases in forest pathology. Obviously, the rapid detection of B. xylophilus is an urgent need for its prevention and cure. We have developed a detection method of B. xylophilus by strand exchange amplification (SEA). This method could detect 105 copies of genomic DNA of B. xylophilus, and it was sufficiently sensitive to detect a single nematode as short as 40 min. Moreover, because the amplification result could be visualized by the naked eyes, the only equipment required throughout the process was a simple isothermal block. Therefore, our method would be a potential for developing on-site detection of B. xylophilus to prevent and control its spread.
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Affiliation(s)
- Caiyan Liu
- College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University
| | - Zengjuan Hu
- Qingdao Agricultural Broadcast and Television School
| | - Xiong Wang
- College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University
| | | | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology
| | - Zonghua Wang
- College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University
| | - Ronggui Li
- College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University
| | - Chao Shi
- College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University
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Zhang H, Okii E, Gotoh E, Shiraishi S. High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan. J Nematol 2018; 50:281-302. [PMID: 30451415 DOI: 10.21307/jofnem-2018-034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes, clearly classified into two clades. Haplotype diversity was 0.83, evidencing a remarkable high diversity within Kyushu. The high genetic differentiation among the 12 populations (0.331) might be due to past invasion and expansion routes of PWN in northeastern and southeastern Kyushu. The distinct genetic composition of populations within the northwestern, central western, and southwestern Kyushu seems to be mostly related to the extinction of pine forests and long-range migration of PWN due to human activity. Overall, direct long PCR and sequencing of single nematode individuals are effective methods for investigating mitochondrial polymorphisms, and these are effective tools for PWN population genetics and other intraspecific studies.
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Affiliation(s)
- Hanyong Zhang
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Erika Okii
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Eiji Gotoh
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Susumu Shiraishi
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Zhou L, Chen F, Ye J, Pan H. Selection of Reliable Reference Genes for RT-qPCR Analysis of Bursaphelenchus mucronatus Gene Expression From Different Habitats and Developmental Stages. Front Genet 2018; 9:269. [PMID: 30083182 PMCID: PMC6064934 DOI: 10.3389/fgene.2018.00269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/02/2018] [Indexed: 12/13/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR), a sensitive technique for gene expression analysis, depends on the stability of the reference genes used for data normalization under different experimental conditions. Bursaphelenchus mucronatus, a pine-parasitic nematode varying in virulence, is widely distributed in natural pine forests throughout the northern hemisphere, but has not been investigated with respect to the identification of reference genes suitable for the normalization of RT-qPCR data. In the present study, eight candidate reference genes were analyzed in B. mucronatus under different habitat conditions and at different developmental stages. The expression stability of these genes was assessed by geNorm, NormFinder, BestKeeper, delta Cq, and RefFinder algorithms. In general, our results identified encoding beta-tubulin as the most stable gene. Moreover, pairwise analysis showed that three reference genes were sufficient to normalize the gene expression data under each set of conditions, with genes encoding beta-tubulin, 18S ribosomal RNA and ubiquitin-conjugating enzyme being the most suitable reference genes for different habitat conditions, whereas genes encoding beta-tubulin, histone, and 18S ribosomal RNA exhibited the most stable expression at different developmental stages. Validation of the selected reference genes was performed by profiling the expression of the fatty acid- and retinol-binding protein gene in different habitats, and by profiling the expression of the arginine kinase gene at different developmental stages. This first systematic analysis for the selection of suitable reference genes for RT-qPCR in B. mucronatus will facilitate future functional analyses and deep mining of genetic resources in this nematode.
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Affiliation(s)
| | - Fengmao Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jianren Ye
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Ali MA, Azeem F, Li H, Bohlmann H. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1699. [PMID: 29046680 PMCID: PMC5632807 DOI: 10.3389/fpls.2017.01699] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- *Correspondence: Muhammad A. Ali ;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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Cardoso JMS, Anjo SI, Fonseca L, Egas C, Manadas B, Abrantes I. Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis. Sci Rep 2016; 6:39007. [PMID: 27941947 PMCID: PMC5150578 DOI: 10.1038/srep39007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022] Open
Abstract
The pinewood nematode, Bursaphelenchus xylophilus, recognized as a worldwide major forest pest, is a migratory endoparasitic nematode with capacity to feed on pine tissues and also on fungi colonizing the trees. Bursaphelenchus mucronatus, the closest related species, differs from B. xylophilus on its pathogenicity, making this nematode a good candidate for comparative analyses. Secretome profiles of B. xylophilus and B. mucronatus were obtained and proteomic differences were evaluated by quantitative SWATH-MS. From the 681 proteins initially identified, 422 were quantified and compared between B. xylophilus and B. mucronatus secretomes and from these, 243 proteins were found differentially regulated: 158 and 85 proteins were increased in B. xylophilus and B. mucronatus secretomes, respectively. While increased proteins in B. xylophilus secretome revealed a strong enrichment in proteins with peptidase activity, the increased proteins in B. mucronatus secretome were mainly related to oxidative stress responses. The changes in peptidases were evaluated at the transcription level by RT-qPCR, revealing a correlation between the mRNA levels of four cysteine peptidases with secretion levels. The analysis presented expands our knowledge about molecular basis of B. xylophilus and B. mucronatus hosts interaction and supports the hypothesis of a key role of secreted peptidases in B. xylophilus pathogenicity.
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Affiliation(s)
- Joana M. S. Cardoso
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sandra I. Anjo
- Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís Fonseca
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Conceição Egas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Isabel Abrantes
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Identifying Virulence-Associated Genes Using Transcriptomic and Proteomic Association Analyses of the Plant Parasitic Nematode Bursaphelenchus mucronatus. Int J Mol Sci 2016; 17:ijms17091492. [PMID: 27618012 PMCID: PMC5037770 DOI: 10.3390/ijms17091492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/05/2016] [Accepted: 08/23/2016] [Indexed: 01/05/2023] Open
Abstract
Bursaphelenchus mucronatus (B. mucronatus) isolates that originate from different regions may vary in their virulence, but their virulence-associated genes and proteins are poorly understood. Thus, we conducted an integrated study coupling RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic data of highly and weakly virulent B. mucronatus isolates during the pathogenic processes. Approximately 40,000 annotated unigenes and 5000 proteins were gained from the isolates. When we matched all of the proteins with their detected transcripts, a low correlation coefficient of r = 0.138 was found, indicating probable post-transcriptional gene regulation involved in the pathogenic processes. A functional analysis showed that five differentially expressed proteins which were all highly expressed in the highly virulent isolate were involved in the pathogenic processes of nematodes. Peroxiredoxin, fatty acid- and retinol-binding protein, and glutathione peroxidase relate to resistance against plant defence responses, while β-1,4-endoglucanase and expansin are associated with the breakdown of plant cell walls. Thus, the pathogenesis of B. mucronatus depends on its successful survival in host plants. Our work adds to the understanding of B. mucronatus' pathogenesis, and will aid in controlling B. mucronatus and other pinewood nematode species complexes in the future.
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Gracianne C, Jan P, Fournet S, Olivier E, Arnaud J, Porte C, Bardou‐Valette S, Denis M, Petit EJ. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift. Evol Appl 2016; 9:1005-16. [PMID: 27606008 PMCID: PMC4999530 DOI: 10.1111/eva.12401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/29/2022] Open
Abstract
Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration-drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies, such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.
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Affiliation(s)
- Cécile Gracianne
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
- VetAgro Sup, UMR 1095, GDECClermont UniversitéClermont‐FerrandFrance
| | - Pierre‐Loup Jan
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
- ESE, Ecology and Ecosystems HealthAgrocampus OuestINRARennesFrance
| | | | - Eric Olivier
- IGEPPINRA, Agrocampus OuestUniversité Rennes 1Le RheuFrance
| | - Jean‐François Arnaud
- UMR CNRS 8198 ÉvolutionÉcologie et PaléontologieUniversité Lille 1 ‐ Sciences et TechnologiesVilleneuve d'Ascq CedexFrance
| | | | | | | | - Eric J. Petit
- ESE, Ecology and Ecosystems HealthAgrocampus OuestINRARennesFrance
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Silva A, Parra P, Campos V, Costa S, Vicente C, Ferreira L, Souza R, Mota M. Genetic diversity of Bursaphelenchus cocophilus in South America. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular characterisation ofBursaphelenchus cocophilus, the causal agent of ‘red ring disease’, is imperative for efficient identification procedures in Brazil and Colombia, because quarantine species such asB. xylophilusandB. mucronatusare already listed in both countries. ITS-1/2 region and D2-D3 segment of LSU rDNA were used to characterise isolates ofB. cocophilusobtained from coconut plantations in Brazil and Colombia. Results from ITS-1/2 and LSU rDNA regions showed that all isolates ofB. cocophilusfrom Brazil and Colombia formed a monophyletic group. The LSU rDNA region indicated that all isolates formed a single monophyletic group with high Bayesian posterior probability (100%). This is the first study on ITS-1/2 for the characterisation ofB. cocophiluspopulations. A species-specific primer was designed for identification ofB. cocophilus.
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Affiliation(s)
- Arinaldo P. Silva
- Department of Plant Pathology, Federal University of Lavras, Lavras, MG, Brazil
- NemaLab/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Pedro P. Parra
- International Centre for Tropical Agriculture (CIAT), Cali, Colombia
| | - Vicente P. Campos
- Department of Plant Pathology, Federal University of Lavras, Lavras, MG, Brazil
| | - Sara S. Costa
- Department of Plant Pathology, Federal University of Lavras, Lavras, MG, Brazil
| | - Cláudia S.L. Vicente
- NemaLab/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
- Department of Environmental Biology, Chubu University, Kasugai, Japan
| | - Letícia G. Ferreira
- Lab. de Pesquisa em Nematologia, CCTA/LEF, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Ricardo M. Souza
- Lab. de Pesquisa em Nematologia, CCTA/LEF, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Manuel Mota
- NemaLab/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, 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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23
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Holguin CM, Baeza JA, Mueller JD, Agudelo P. High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States. Ecol Evol 2015; 5:2929-44. [PMID: 26306177 PMCID: PMC4541996 DOI: 10.1002/ece3.1568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 11/17/2022] Open
Abstract
Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.
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Affiliation(s)
- Claudia M Holguin
- Department of Agricultural and Environmental Sciences, Clemson UniversityClemson, South Carolina, 29634
| | - Juan A Baeza
- Department of Biological Sciences, Clemson UniversityClemson, South Carolina, 29634
| | - John D Mueller
- Edisto Research and Education Center, Clemson UniversityBlackville, South Carolina, 29817
| | - Paula Agudelo
- Department of Agricultural and Environmental Sciences, Clemson UniversityClemson, South Carolina, 29634
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24
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Mallez S, Castagnone C, Espada M, Vieira P, Eisenback JD, Harrell M, Mota M, Aikawa T, Akiba M, Kosaka H, Castagnone-Sereno P, Guillemaud T. Worldwide invasion routes of the pinewood nematode: What can we infer from population genetics analyses? Biol Invasions 2014. [DOI: 10.1007/s10530-014-0788-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Zhao L, Mota M, Vieira P, Butcher RA, Sun J. Interspecific communication between pinewood nematode, its insect vector, and associated microbes. Trends Parasitol 2014; 30:299-308. [DOI: 10.1016/j.pt.2014.04.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/08/2014] [Accepted: 04/11/2014] [Indexed: 01/23/2023]
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26
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Čermák V, Čermák V, Vieira P, Čermák V, Vieira P, Čudejková M, Čermák V, Vieira P, Čudejková M, Gaar V, Čermák V, Vieira P, Čudejková M, Gaar V, Tománková K, Čermák V, Vieira P, Čudejková M, Gaar V, Tománková K, Mikušková K, Čermák V, Vieira P, Čudejková M, Gaar V, Tománková K, Mikušková K, Eisenback JD, Čermák V, Vieira P, Čudejková M, Gaar V, Tománková K, Mikušková K, Eisenback JD, Mota M. Bursaphelenchus hofmanni Braasch, 1998 associated with peat growth substrate in hops nurseries in the Czech Republic. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Vladimir Gaar
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Vladimir Gaar
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Tománková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Vladimir Gaar
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Tománková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Mikušková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Vladimir Gaar
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Tománková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Mikušková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Jonathan D. Eisenback
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Václav Čermák
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Paulo Vieira
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Mária Čudejková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Šlechtitelů 586/11, 779 00 Olomouc, Czech Republic
| | - Vladimir Gaar
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Tománková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Kateřina Mikušková
- State Phytosanitary Administration, Division of Diagnostics, Šlechtitelů 773/23, 779 00 Olomouc, Czech Republic
| | - Jonathan D. Eisenback
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Manuel Mota
- Lab. Nematologia/ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
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27
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Figueiredo J, Simões MJ, Gomes P, Barroso C, Pinho D, Conceição L, Fonseca L, Abrantes I, Pinheiro M, Egas C. Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes. PLoS One 2013; 8:e83542. [PMID: 24391785 PMCID: PMC3877046 DOI: 10.1371/journal.pone.0083542] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 11/05/2013] [Indexed: 11/18/2022] Open
Abstract
The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.
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Affiliation(s)
- Joana Figueiredo
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Maria José Simões
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Paula Gomes
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Cristina Barroso
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Diogo Pinho
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Luci Conceição
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Luís Fonseca
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Miguel Pinheiro
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Conceição Egas
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
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28
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Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales. Mol Phylogenet Evol 2013; 70:120-9. [PMID: 24076248 DOI: 10.1016/j.ympev.2013.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/22/2022]
Abstract
Tandemly repeated sequences known as satellite DNA (satDNA) generally exhibit complex evolutionary patterns of concerted evolution in which mutations are homogenized and fixed in a stochastic process of molecular drive. Here, the nucleotidic variability of the MspI satDNA family of the pinewood nematode Bursaphelenchus xylophilus is analyzed in order to understand the evolutionary dynamics of satDNA at the intraspecific level. A total of 425 MspI monomer units, either PCR-amplified from isolates of local (Peninsula of Setúbal, Portugal) or worldwide origin, or retrieved from the B. xylophilus genome sequence, were characterized and compared. Whatever their origin, sliding window analysis of sequence variability patterns among monomers revealed low, moderate and highly variant domains, indicating that variable levels of evolutionary constraint may act upon the entire monomers. The phylogenetic inference based on the different sets of MspI satDNA family for this species shows a broad polymorphism of the individual monomers, which were distributed into four main clusters. However, such clustering appeared independent from the geographic origin of the nematodes, and could not discriminate isolates or groups of geographically close isolates. Rather, the formation of different phylogenetic groups within this satDNA family suggests an a priori embodying of a set of diverging repeats from a common ancestor satDNA library, which have been differently amplified along the evolutionary pathway of this species. The present work improves knowledge on the evolutionary dynamics of satDNA at the intraspecific level, and provides new information on satDNA sequence variability among natural populations sampled at a local geographic scale.
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Moreira C, van Asch B, Fonseca L, Pereira-Castro I, Silva R, Azevedo L, Mota M, Abrantes I, Amorim A, Pereira F. The mitochondrial genome of the pinewood nematode (Bursaphelenchus xylophilus) lineage introduced in Europe. ACTA ACUST UNITED AC 2013; 25:420-1. [PMID: 23841612 DOI: 10.3109/19401736.2013.809438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The pinewood nematode (PWN) Bursaphelenchus xylophilus is the causative agent of pine wilt disease and the greatest biological threat to conifer forests worldwide. Here we describe the near-complete mitochondrial DNA (mtDNA) sequence (12,945 bp) of the PWN lineage recently introduced in Europe. The absence of polymorphisms across the mtDNA of three Portuguese isolates suggests that a single mitochondrial lineage was introduced in southwestern Europe. We also found that Portuguese isolates have an incomplete stop codon (TA) at COX3, while the reference mtDNA from a South Korean isolate has a complete stop codon (TAA). Moreover, two insertion/deletion polymorphisms change the ND4 protein in a stretch of seven amino acids, and a polymorphic mononucleotide repeat alters the predicted structure of the tyrosine tRNA in different geographical isolates. Overall, the new PWN mtDNA sequence provides a basis for studying the European dispersion of this important invasive species.
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Affiliation(s)
- Cláudia Moreira
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP) , Porto , Portugal
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