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Gendron EM, Sevigny JL, Byiringiro I, Thomas WK, Powers TO, Porazinska DL. Nematode mitochondrial metagenomics: A new tool for biodiversity analysis. Mol Ecol Resour 2023. [PMID: 36727264 DOI: 10.1111/1755-0998.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023]
Abstract
DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.
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Affiliation(s)
- Eli M Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Innocent Byiringiro
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - W Kelley Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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Pratylenchus Araucensis (Rhabditida: Pratylenchidae) a Widely Distributed Nematode in Musa Spp. from Colombia. J Nematol 2023; 54:20220057. [PMID: 36742266 PMCID: PMC9871600 DOI: 10.2478/jofnem-2022-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Indexed: 01/09/2023] Open
Abstract
Pratylenchus is one of the most limiting nematodes of Musaceae production in the world. Knowledge of the nematode species is one of the requirements for its management in the field. This study aimed to identify up to the species level Pratylenchus populations associated with plantain and banana crops in the states of Caldas, Quindío, and Valle del Cauca in Colombia. In these regions, Pratylenchus has been reported to affect these crops in the past, but with records of the nematode only up to the genus level. For this purpose, five populations of Pratylenchus extracted from samples composed of roots and rhizospheric soil, four from plantain and one from banana, were identified through morphological, morphometric, and molecular analysis (sequencing of the D2-D3 of rRNA and cytochrome oxidase subunit I of mtDNA). All populations were identified as P. araucensis, a species reported previously in eastern Colombia, and one that the present study found in the center and southwest of the country, indicating that this species of nematode is widely distributed in the Musaceae-producing areas of Colombia. The present study reports the first COI mtDNA sequences for this species of nematode.
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3
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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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Wendt EW, Malabarba LR, Braga MP, Boeger WA, Landis M, Carvalho TP. Phylogeny, species delimitation, and ecological and morphological diversity of Characithecium (Monogenoidea: Dactylogyridae). Parasitology 2022:1-54. [PMID: 35236513 DOI: 10.1017/s0031182022000221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Characithecium (Monogenoidea, Dactylogyridae) is a genus containing nine species that live on the gills of a characid clade containing genera Astyanax, Andromakhe, Psalidodon and Oligosarcus (Characiformes, Characidae) in South and Central America. Earlier studies suggest a tight coevolutionary history between these parasites and their hosts mainly due to the phylogenetic proximity between these genera of fish. Hence, this study explores phylogenetic relationships, species limits and extrinsic factors (geography and ecology) explaining parasite prevalence. To understand the evolutionary history of the genus, we constructed a time-calibrated phylogenetic hypothesis, which includes eight of the nine known species of Characithecium sampled from a broad spectrum of host species. The phylogeny supports the monophyly of Characithecium, with its most recent common ancestor dating from the Miocene. Using generalized mixed-yule coalescent and Bayesian Poisson tree process methods, species delimitation analyses suggested fewer species than the proposed delimitation based on morphology alone, recovering four and six entities, respectively. The results indicate that species of Characithecium have wider geographical and host distribution and higher prevalence on Oligosarcus species compared to Astyanax and Psalidodon. Correlation between parasite prevalence and biotic and abiotic traits, based on generalized linear models, indicates that the frequency of occurrence of different species of Characithecium is associated with distinct factors, such as host genus, high altitudes, rivers and streams, and different ecoregions. Our results suggest that species of Characithecium are highly opportunistic, exploring resources in different manner as our data reveal the ability of these parasites to explore a diverse environment of variable biotic (e.g. hosts) and abiotic features.
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Affiliation(s)
- Emília W Wendt
- Laboratório de Ictiologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves, 9500, Bloco 4, prédio 43435, 91501-970Porto Alegre, RS, Brazil
| | - Luiz R Malabarba
- Laboratório de Ictiologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves, 9500, Bloco 4, prédio 43435, 91501-970Porto Alegre, RS, Brazil
| | - Mariana P Braga
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Walter A Boeger
- Biological Interactions and Departamento de Zoologia, Centro Politécnico, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Caixa Postal 19073, CEP 81531-980, Curitiba, Paraná, Brazil
| | - Michael Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tiago P Carvalho
- Laboratório de Ictiologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves, 9500, Bloco 4, prédio 43435, 91501-970Porto Alegre, RS, Brazil
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 N° 43-82, Bogotá D.C., Colombia
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Naeini FS, Taheri ZM. First report of root-lesion nematode, Pratylenchus oleae from pistachio in Iran. J Nematol 2021; 53:e2021-103. [PMID: 34901873 PMCID: PMC8662977 DOI: 10.21307/jofnem-2021-103] [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: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
Pistachio, Pistacia vera is one of the most important cash crops in Iran that is scattered in arid and semi-arid regions. During a survey of plant-parasitic nematodes of pistachio in Ardakan city in Yazd Province, a species of root-lesion nematode was isolated and identified by morphological, morphometrical, and molecular methods as Pratylenchus oleae Palomares-Rius et al., 2014. This species was isolated from several pistachio trees rhizosphere regarding to molecular analysis, D2–D3 expansion segments of 28S rRNA was amplified by PCR and sequenced. The sequence was deposited in GenBank (Accession No. MW338666). Along with the related phylogenetic analysis, placed this species in a monophyletic clade with other Pratylenchus oleae isolates, based on Bayesian inference (BI) phylogeny. A PCR reaction with the P. oleae specific primer set produced a 547 bp fragment. This is the first report of P. oleae infecting Pistachio tree in the world.
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Affiliation(s)
- Farhad Saeidi Naeini
- Nematology Department, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension, Organization (AREEO), Tehran, Iran
| | - Zahra Majd Taheri
- Nematology Department, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension, Organization (AREEO), Tehran, Iran
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Lax P, Gonzalez‐Ittig RE, Rondan Dueñas JC, Andrade AJ, Gardenal CN, Franco J, Doucet ME. Decrypting species in the
Nacobbus aberrans
(Nematoda: Pratylenchidae) complex using integrative taxonomy. ZOOL SCR 2021. [DOI: 10.1111/zsc.12494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Paola Lax
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Raúl E. Gonzalez‐Ittig
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Juan C. Rondan Dueñas
- Laboratorio de Biología Molecular Pabellón CEPROCOR Santa María de Punilla Córdoba, Argentina
| | - Alberto J. Andrade
- Instituto de Biología de la Altura Universidad Nacional de Jujuy San Salvador de Jujuy Argentina
| | - Cristina N. Gardenal
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | | | - Marcelo E. Doucet
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
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Singh PR, Karssen G, Couvreur M, Subbotin SA, Bert W. Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes. PLANTS (BASEL, SWITZERLAND) 2021; 10:408. [PMID: 33671787 PMCID: PMC7926417 DOI: 10.3390/plants10020408] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/18/2023]
Abstract
Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.
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Affiliation(s)
- Phougeishangbam Rolish Singh
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
- National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Marjolein Couvreur
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA;
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian, Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
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Morphological and Molecular Characterization of Pratylenchus dakotaensis n. sp. (Nematoda: Pratylenchidae), a New Root-Lesion Nematode Species on Soybean in North Dakota, USA. PLANTS 2021; 10:plants10010168. [PMID: 33477266 PMCID: PMC7829955 DOI: 10.3390/plants10010168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022]
Abstract
Root-lesion nematodes (Pratylenchus spp.) of the genus Pratylenchus Filipjev, 1936, are among the most important nematode pests on soybean (Glycine max (L.) Merr.), along with soybean cyst and root-knot nematodes. In May 2015 and 2016, a total of six soil samples were collected from a soybean field in Walcott, Richland County, ND and submitted to the Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL), USDA, ARS, MD for analysis. Later, in 2019, additional nematodes recovered from a greenhouse culture on soybean originally from the same field were submitted for further analysis. Males, females, and juveniles of Pratylenchus sp. were recovered from soil and root samples and were examined morphologically and molecularly. DNA from single nematodes were extracted, and the nucleotides feature of three genomic regions targeting on the D2–D3 region of 28S rDNA and ITS rDNA and mitochondrial cytochrome oxidase subunit I (COX1) gene were characterized. Phylogeny trees were constructed to ascertain the relationships with other Pratylenchus spp., and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to provide a rapid and reliable differentiation from other common Pratylenchus spp. Molecular features indicated that it is a new, unnamed Pratylenchus sp. that is different from morphologically closely related Pratylenchus spp., including P. convallariae, P. pratensis, P. fallax, and P. flakkensis. In conclusion, both morphological and molecular observations indicate that the North Dakota isolate on soybean represents a new root-lesion nematode species which is named and described herein as Pratylenchus dakotaensis n. sp.
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Bucki P, Qing X, Castillo P, Gamliel A, Dobrinin S, Alon T, Braun Miyara S. The Genus Pratylenchus (Nematoda: Pratylenchidae) in Israel: From Taxonomy to Control Practices. PLANTS 2020; 9:plants9111475. [PMID: 33147883 PMCID: PMC7716202 DOI: 10.3390/plants9111475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022]
Abstract
Due to Israel’s successful agricultural production and diverse climatic conditions, plant-parasitic nematodes are flourishing. The occurrence of new, previously unidentified species in Israel or of suggested new species worldwide is a consequence of the continuous withdrawal of efficient nematicides. Among plant-parasitic nematodes, migratory endoparasitic species of the genus Pratylenchus are widely distributed in vegetable and crop fields in Israel and are associated with major reductions in quality and yield. This review focuses on the occurrence, distribution, diagnosis, pathogenicity, and phylogeny of all Pratylenchus species recorded over the last few decades on different crops grown throughout Israel—covering early information from nematologists to recent reports involving the use of molecular phylogenetic methodologies. We explore the accepted distinction between Pratylenchus thornei and Pratylenchus mediterraneus isolated from Israel’s northern Negev region, and address the confusion concerning the findings related to these Pratylenchus species. Our recent sampling from the northern Negev revealed the occurrence of both P. thornei and P. mediterraneus on the basis of molecular identification, indicating P. mediterraneus as a sister species of P. thornei and their potential occurrence in a mixed infection. Finally, the efficiencies of common control measures taken to reduce Pratylenchus’ devastating damage in protected crops and field crops is discussed.
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Affiliation(s)
- Patricia Bucki
- Volcani Center, Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Rishon Lezion 15159, Israel; (P.B.); (X.Q.)
| | - Xue Qing
- Volcani Center, Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Rishon Lezion 15159, Israel; (P.B.); (X.Q.)
- Department of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Pablo Castillo
- Institute for Sustainable Agriculture, Spanish National Research Council, 14004 Cordoba, Spain;
| | - Abraham Gamliel
- Volcani Center, Laboratory for Pest Management Research, Institute of Agricultural Engineering, ARO, Rishon Lezion 15159, Israel;
| | - Svetlana Dobrinin
- Extension Service (Shaham), Israel Ministry of Agriculture and Rural Development, Rishon Lezion 15159, Israel; (S.D.); (T.A.)
| | - Tamar Alon
- Extension Service (Shaham), Israel Ministry of Agriculture and Rural Development, Rishon Lezion 15159, Israel; (S.D.); (T.A.)
| | - Sigal Braun Miyara
- Volcani Center, Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Rishon Lezion 15159, Israel; (P.B.); (X.Q.)
- Correspondence:
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10
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Cai R, Archidona‐Yuste A, Cantalapiedra‐Navarrete C, Palomares‐Rius JE, Castillo P. New evidence of cryptic speciation in the family Longidoridae (Nematoda: Dorylaimida). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12393] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ruihang Cai
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
- Laboratory of Plant Nematology Institute of Biotechnology College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Antonio Archidona‐Yuste
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
- Department of Ecological Modelling Helmholtz Centre for Environmental Research ‐ UFZ Leipzig Germany
| | - Carolina Cantalapiedra‐Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
| | - Juan E. Palomares‐Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
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Handoo ZA, Skantar AM, Kantor MR, Hafez SL, Hult MN. Molecular and morphological characterization of the amaryllis lesion nematode, Pratylenchus hippeastri (Inserra et al., 2007), from California. J Nematol 2020; 52:1-5. [PMID: 32628824 PMCID: PMC7366837 DOI: 10.21307/jofnem-2020-058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 11/11/2022] Open
Abstract
Root-lesion nematodes (Pratylenchus spp.) are among the most important nematode pests on grapevine along with root-knot, dagger, and ring nematodes. In 2019, two samples of both soil and roots were collected from a vineyard in Delano, Kern County, California and submitted to the United States Department of Agriculture, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, for identification purposes. Females and juveniles of Pratylenchus sp. were recovered from the root and soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Both morphological observations and molecular analysis of internal transcribed spacer (ITS), 28S large subunit ribosomal DNA, and mitochondrial cytochrome oxidase (COI) sequences indicated that the specimens recovered from the soil and roots were Pratylenchus hippeastri. To the best of the authors' knowledge, this is the first report of P. hippeastri from California including the first record of this species on grapevine and the second state record in North America. Damages caused by nematodes cannot be over-emphasized, although economic importance of P. hippeastri has never been established. Hence, there is an urgent need to investigate the economic impact of this nematode in vineyards in California State in order to develop sustainable management strategies. Root-lesion nematodes (Pratylenchus spp.) are among the most important nematode pests on grapevine along with root-knot, dagger, and ring nematodes. In 2019, two samples of both soil and roots were collected from a vineyard in Delano, Kern County, California and submitted to the United States Department of Agriculture, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, for identification purposes. Females and juveniles of Pratylenchus sp. were recovered from the root and soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Both morphological observations and molecular analysis of internal transcribed spacer (ITS), 28S large subunit ribosomal DNA, and mitochondrial cytochrome oxidase (COI) sequences indicated that the specimens recovered from the soil and roots were Pratylenchus hippeastri. To the best of the authors’ knowledge, this is the first report of P. hippeastri from California including the first record of this species on grapevine and the second state record in North America. Damages caused by nematodes cannot be over-emphasized, although economic importance of P. hippeastri has never been established. Hence, there is an urgent need to investigate the economic impact of this nematode in vineyards in California State in order to develop sustainable management strategies.
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Affiliation(s)
- Zafar A. Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD 20705
| | - Andrea M. Skantar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD 20705
| | - Mihail R. Kantor
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD 20705
| | | | - Maria N. Hult
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD 20705
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12
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Bai M, Qing X, Qiao K, Ning X, Xiao S, Cheng X, Liu G. Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species. J Nematol 2020; 52:1-12. [PMID: 32330378 PMCID: PMC7266042 DOI: 10.21307/jofnem-2020-038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 11/28/2022] Open
Abstract
Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships.
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Affiliation(s)
- Mengxin Bai
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University , Nanjing, 210095, China
| | - Kaikai Qiao
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China ; State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, 455000, Anyang, Henan, China
| | - Xulan Ning
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China
| | - Shun Xiao
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China
| | - Xi Cheng
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China
| | - Guokun Liu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University , 350002, Fuzhou, Fujian, China
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Qing X, Wang M, Karssen G, Bucki P, Bert W, Braun-Miyara S. PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes. Bioinformatics 2019; 36:1052-1056. [DOI: 10.1093/bioinformatics/btz707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/31/2019] [Accepted: 09/11/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Motivation
The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background.
Results
The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward.
Availability and implementation
The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xue Qing
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Meng Wang
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Gerrit Karssen
- National Plant Protection Organization, Wageningen Nematode Collection, Wageningen HC, The Netherlands
| | - Patricia Bucki
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Wim Bert
- Department of Biology, Nematology Research Unit, Ghent University, Ghent, Belgium
| | - Sigal Braun-Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
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14
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Ozbayrak M, Todd T, Harris T, Higgins R, Powers K, Mullin P, Sutton L, Powers T. A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America. J Nematol 2019. [DOI: 10.21307/jofnem-2019-081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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