1
|
Mwamula AO, Kwon OG, Kwon C, Kim YS, Kim YH, Lee DW. A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA. THE PLANT PATHOLOGY JOURNAL 2024; 40:171-191. [PMID: 38606447 PMCID: PMC11016563 DOI: 10.5423/ppj.oa.01.2024.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/13/2024]
Abstract
Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.
Collapse
Affiliation(s)
- Abraham Okki Mwamula
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Oh-Gyeong Kwon
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
| | - Chanki Kwon
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Yi Seul Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Young Ho Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Dong Woon Lee
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
2
|
Archidona-Yuste A, Clavero-Camacho I, Ruiz-Cuenca AN, Cantalapiedra-Navarrete C, Liebanas G, Castillo P, Palomares-Rius JE. The more we search, the more we find: discovering and expanding the biodiversity in the ring nematode genus Xenocriconemella De Grisse and Loof, 1965 (Nematoda: Criconematidae). ZOOLOGICAL LETTERS 2024; 10:8. [PMID: 38528566 DOI: 10.1186/s40851-024-00230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024]
Abstract
The ring nematode genus Xenocriconemella De Grisse and Loof, 1965 comprises only one nominal species, Xenocriconemella macrodora (Taylor, 1936) De Grisse and Loof, 1965. The initial objective of the present study was to investigate the morphological-morphometric and molecular diversity of 28 X. macrodora populations in the Iberian Peninsula associated with tree forests (mainly Quercus spp.). However, a detailed integrative taxonomic analysis (morphological-morphometric and molecular data) from each population and analysis of this data using principal component analysis (PCA) for morphometric data (including these 28 populations and other 25 X. macrodora populations around the world) and molecular and phylogenetic species delimitation methods revealed that X. macrodora forms a species complex. This species complex is composed by species that are morphometricly and morphologically similar, but clearly different at the molecular level. Three new species are described applying integrative taxonomy, namely as Xenocriconemella iberica sp. nov., Xenocriconemella paraiberica sp. nov. and Xenocriconemella pradense sp. nov. However, the molecular diversity of this species in USA and Italy confirmed that additional species are likely present in this species complex, and the diversity of this group may be higher than expected. The study of X. macrodora topotypes can clarify the position of this species using molecular markers under an integrative approach.
Collapse
Affiliation(s)
- A Archidona-Yuste
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain.
| | - I Clavero-Camacho
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - A N Ruiz-Cuenca
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
- Department of Animal, Plant Biology and Ecology, University of Jaén, Campus Las Lagunillas, Jaén, Spain
| | - C Cantalapiedra-Navarrete
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - G Liebanas
- Department of Animal, Plant Biology and Ecology, University of Jaén, Campus Las Lagunillas, Jaén, Spain
| | - P Castillo
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| | - J E Palomares-Rius
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avda. Menendez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004, Córdoba, Spain
| |
Collapse
|
3
|
Archidona-Yuste A, Palomares-Rius JE, Clavero-Camacho I, Cantalapiedra-Navarrete C, Liébanas G, Castillo P. A Blind-Identification Test on Criconema annuliferum (de Man, 1921) Micoletzky, 1925 Species Complex Corroborate the Hyper-Cryptic Species Diversity Using Integrative Taxonomy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1044. [PMID: 36903905 PMCID: PMC10005498 DOI: 10.3390/plants12051044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Ring nematodes are obligate ectoparasites on crops and natural herbaceous and woody plants, and some species are of economic importance and cause damage to roots of several crops. Recent integrative taxonomical analyses recognized the existence of two cryptic species within the Criconema annuliferum morphotype in Spain. In this study, we corroborated that morphometric, morphological and a multi-locus analysis (including the ribosomal markers D2-D3 expansion segments of 28S rRNA, ITS rRNA, 18S RNA, and the mitochondrial DNA cytochrome oxidase I gene) identified a new lineage clearly separated from C. annuliferum, C. paraannuliferum and C. plesioannuliferum. The new lineage was described herein as Criconema pseudoannuliferum sp. nov., confirming that C. annuliferum species complex species complex comprises a hyper-cryptic species complex. This research analysed soil samples from the rhizosphere of maritime pine (Pinus pinaster Ait.) forests in Bermeja-Crestellina Mountain, located at the western part of Málaga province, southern Spain. The integrative taxonomical analyses revealed the occurrence of a new cryptic species identified using females, males and juveniles with detailed morphology, morphometry and molecular markers, described herein as Criconema pseudoannuliferum sp. nov. All molecular markers (D2-D3, ITS, 18S and COI) were obtained from the same individual that was also used for morphological and morphometric analyses. This research demonstrated the hidden diversity within the C. annuliferum species complex species complex can reach to four lineages under ribosomal and mitochondrial gene markers for one morphospecies group, which includes four species, viz. C. annuliferum, C. paraannuliferum, C. plesioannuliferum, and C. pseudoannuliferum sp. nov. Criconema pseudoannuliferum sp. nov. was detected in moderate soil density in two maritime pine forests (5 and 25 nematodes/500 cm3 of soil) suggesting that does not cause damage to maritime pine.
Collapse
Affiliation(s)
- Antonio Archidona-Yuste
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Juan Emilio Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Ilenia Clavero-Camacho
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Carolina Cantalapiedra-Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| | - Gracia Liébanas
- Department of Animal Biology, Plant Biology and Ecology, University of Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain
| |
Collapse
|
4
|
Mwamula AO, Lee SM, Jung YH, Lee HW, Kim YS, Kim YH, Lee DW. Morphological and Molecular Characterization of Diplogasteroides sp., a Cryptic Population of the Haslacheri Group (Diplogastridae), and Parasitorhabditis terebranus (Rhabditidae) from Korea. J Nematol 2023; 55:20230017. [PMID: 37342200 PMCID: PMC10277748 DOI: 10.2478/jofnem-2023-0017] [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: 01/29/2023] [Indexed: 06/22/2023] Open
Abstract
Diplogasteroides sp., a cryptic population of D. haslacheri, and Parasitorhabditis terebranus were reported from the frass of Monochamus alternatus galleries in dead Pinus thunbergii for the first time in Korea. Females and males are morphologically characterized and their linked DNA barcodes (18S-rRNA, 28S-rRNA, ITS-rRNA and COI) supplied. Females and males of the two species from Korea conform to the original species descriptions from Europe and the USA, with variations in a few details in morphometrics. Specifically, Diplogasteroides sp. is morphologically very similar to D. haslacheri. However, it cannot be designated as D. haslacheri due to the existence of cryptic species complex within the haslacheri group (D. haslacheri, D. asiaticus, D. nix, D. andrassyi, and D. carinthiacus), a condition requiring hybridization studies to test species identity within the group. Based on analysis of COI sequences, differences among these cryptic species are evident. Thus, in addition to hybridization tests, the COI might be a powerful DNA barcoding marker for the precise identification of these cryptic species within the genus. Additionally, this is the first molecular characterization of P. terebranus, and the species is herein recorded for the first time outside its type locality.
Collapse
Affiliation(s)
- Abraham Okki Mwamula
- Department of Entomology, Kyungpook National University, Sangju, 37224, Republic of Korea
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju37224, Republic of Korea
| | | | | | - Ho-wook Lee
- Department of Ecological Science, Kyungpook National University, Sangju, 37224, Republic of Korea
| | - Yi Seul Kim
- Department of Entomology, Kyungpook National University, Sangju, 37224, Republic of Korea
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju37224, Republic of Korea
| | - Young Ho Kim
- Department of Entomology, Kyungpook National University, Sangju, 37224, Republic of Korea
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju37224, Republic of Korea
| | - Dong Woon Lee
- Department of Entomology, Kyungpook National University, Sangju, 37224, Republic of Korea
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju37224, Republic of Korea
- Department of Ecological Science, Kyungpook National University, Sangju, 37224, Republic of Korea
| |
Collapse
|
5
|
Remarks on phylogeny and molecular variations of criconematid species (Nematoda: Criconematidae) with case studies from Vietnam. Sci Rep 2022; 12:14832. [PMID: 36050334 PMCID: PMC9437051 DOI: 10.1038/s41598-022-18004-2] [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: 04/24/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
The family Criconematidae is a remarkable group of nematodes, containing roughly 600 nominal root-ectoparasitic species, of which many species are known to be significant agricultural pests. Strikingly, our phylogenetic analyses based on 18S, D2-D3 of 28S rRNA, and COI mtDNA sequences of criconematid species, supported by tree topology tests (SH and AU tests), revealed that almost all studied genera, including Criconema, Ogma, Crossonema, Discocriconema, Hemicriconemoides, Criconemoides, Mesocriconema, and Lobocriconema, are not monophyletic groups, a finding that is partly contrary to those of previous studies on these groups. Our results suggest that key morphological characters used in the classification of Criconematidae are the consequence of convergent evolution. It is clear from our studies that the species status of at least 40 sequences of criconematid species from GenBank must be either revised or reconsidered, with analyses based on a polyphasic approach that includes different tree- and distance-based molecular species-delimitation methods (bPTP, GMYC, ABGD1, and ABGD2). Our studies found the ABGD2 output of the automatic barcode method to agree remarkably well with established species delimitations, while in general, the four species-delimitation results corresponding to three barcode regions forwarded significantly more putative species compared to those originally considered. This study also characterised for the first time the populations of Criconemoides myungsugae and Discocriconemella hensungica associated with Vietnamese ginseng, one of the most precious and rare ginseng varieties in the world. Although these populations are morphologically in agreement with the original descriptions of C. myungsugae and D. hengsungica, their molecular data display notable variations compared to the sequences deposited in GenBank. These species demonstrate clearly the immense molecular variations that can be observed in several species of the family Criconematidae.
Collapse
|
6
|
Mwamula AO, Kim Y, Kim YH, Lee HW, Kim YH, Lee DW. Molecular Characterization of Filenchus cylindricus (Thorne & Malek, 1968) Niblack & Bernard, 1985 (Tylenchida: Tylenchidae) from Korea, with Comments on Its Morphology. THE PLANT PATHOLOGY JOURNAL 2022; 38:323-333. [PMID: 35953052 PMCID: PMC9372097 DOI: 10.5423/ppj.oa.02.2022.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/14/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Filenchus cylindricus (Thorne & Malek, 1968) Niblack & Bernard, 1985 was reported from the sandy rhizospheric soils of Poa pratensis and for the first time in Korea. Females and males are molecularly characterized and morphological and morphometric data supplied. Identification was made using an integrative approach considering morphological characteristics and inferences drawn from the analyses of the D2-D3 expansion segment of 28S rRNA and ITS1-5.8S-ITS2 of rRNA partial sequences. Females and males from Korea conform to the type descriptions and also to subsequent species descriptions from Iowa and Colorado USA, Sudan and Pakistan. Despite the close morphological and morphometric similarities with F. thornei (Andrássy, 1954) Andrássy, 1963, the two species can be adequately differentiated based on molecular data inference.
Collapse
Affiliation(s)
- Abraham Okki Mwamula
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566,
Korea
| | - Yiseul Kim
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
| | - Yeong Ho Kim
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
| | - Ho-wook Lee
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
| | - Young Ho Kim
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566,
Korea
| | - Dong Woon Lee
- Department of Ecological Science, Kyungpook National University, Sangju 37224,
Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566,
Korea
| |
Collapse
|
7
|
Clavero-Camacho I, Palomares-Rius JE, Cantalapiedra-Navarrete C, Castillo P, Liébanas G, Archidona-Yuste A. A Proposed New Species Complex within the Cosmopolitan Ring Nematode Criconema annuliferum (de Man, 1921) Micoletzky, 1925. PLANTS (BASEL, SWITZERLAND) 2022; 11:1977. [PMID: 35956456 PMCID: PMC9370717 DOI: 10.3390/plants11151977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Ring nematodes are obligate ectoparasites on cultivated and wild herbaceous and woody plants, inhabiting many types of soil, but particularly sandy soils. This study explored the morphometrical and molecular diversity of ring nematodes resembling Criconema annuliferum in 222 soil samples from fruit crops in Spain, including almond, apricot, peach and plum, as well as populations from cultivated and wild olives, and common yew. Ring nematodes of the genus Criconema were detected in 12 samples from under Prunus spp. (5.5%), showing a low to moderate nematode soil densities in several localities from southeastern and northeastern Spain. The soil population densities of Criconema associated with Prunus spp. ranged from 1 nematode/500 cm3 of soil in apricot at Sástago (Zaragoza province) to 7950 and 42,491 nematodes/500 cm3 of soil in peach at Ricla and Calasparra (Murcia province), respectively. The integrative taxonomical analyses reveal the presence of two cryptic species identified using females, males (when available), and juveniles with detailed morphology, morphometry, and molecular markers (D2-D3, ITS, 18S, and COI), described herein as Criconema paraannuliferum sp. nov. and Criconema plesioannuliferum sp. nov. All molecular markers from each species were obtained from the same individuals, and these individuals were also used for morphological and morphometric analyses. Criconema paraannuliferum sp. nov. was found in a high soil density in two peach fields (7950 and 42,491 nematodes/500 cm3 of soil) showing the possibility of being pathogenic in some circumstances.
Collapse
Affiliation(s)
- Ilenia Clavero-Camacho
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Juan Emilio Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Carolina Cantalapiedra-Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3, 14004 Córdoba, Spain; (I.C.-C.); (J.E.P.-R.); (C.C.-N.); (P.C.)
| | - Gracia Liébanas
- Department of Animal Biology, Plant Biology and Ecology, University of Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain;
| | - Antonio Archidona-Yuste
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, 14004 Córdoba, Spain
| |
Collapse
|
8
|
Six First Reports of Pin Nematodes from Portugal, with an Update of the Systematics, Genetic Diversity, and Phylogeny of the Genus Paratylenchus (Nematoda: Tylenchulidae). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040343] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pin nematodes (Paratylenchus spp.) currently comprise 132 species of polyphagous plant ectoparasites with at least seven species that are plant pathogenic emphasizing the need for correct identification to establish an appropriate management strategy. Sequences of highly conserved regions of ribosomal and mitochondrial RNA genes are a powerful species-level diagnostic tool within Tylenchulidae. A nematological survey was conducted from 2019 to 2021 in commercial vineyards distributed in four major wine-producing regions in the Central and South Portugal. Nine populations of Paratylenchus spp. were isolated from the rhizosphere of grapevines that were characterized from morphological data and molecular phylogenetic analysis using two rRNA genes (D2–D3 expansion segments of the 28S, and partial 18S) and a region partial of the COI mtRNA gene. Contrasting morphological hypotheses with molecular data provided rapid detection of six species, specifically P. goodeyi, P. hamatus, P. pedrami, P. tenicaudatus, P. variabilis, and P. veruculatus. Bayesian inference (BI) phylogenetic trees for these molecular markers established phylogenetic relationships underscore the importance of using genomic and molecular phylogenetic data for accurate pin nematode identification at the species level. To our knowledge, this is the first report of Paratylenchus spp. in Portugal, extending the geographical distribution of these species in the Mediterranean Basin, and the first record of P. goodeyi, P. pedrami, P.variabilis, P. veruculatus and P. tenicaudatus parasitizing grapevine.
Collapse
|
9
|
Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
|
10
|
Morphological and Molecular Characterization of Nothotylenchus medians and N. similis (Nematoda: Anguinidae) from Southern Alberta, Canada. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The nematode family, Anguinidae, is a diverse group of polyphagous nematodes, generally known as fungal feeders or parasites of aerial plant parts. Here, we present the morphological and molecular characterization of adult females of two Nothotylenchus species, N. medians and N. similis, along with host association and geographical distribution data of the genus. Both species are recorded as new reports from Canada and designated as reference populations for future studies. Morphological or morphometrical variation was not observed in the Canadian population of N. medians and N. similis, in comparison with the original description. Phylogenetic analyses based on 18S and D2–D3 of 28S genes placed both species within Anguinidae. Since the biology of the genus Nothotylenchus has not been rigorously characterized, the habitat and distribution information presented in this study will shed some light on the ecology of these nematodes. Notably, the detection of N. medians and N. similis in our nematode inventory survey indicates that considerable Nothotylenchus diversity is hidden in these soils. Consequently, increased surveys and more in-depth research are needed to explore the full diversity of anguinids inhabiting these cultivated areas.
Collapse
|
11
|
Nguyen HT, Nguyen TD, Le TML, Trinh QP. Integrative taxonomy of Mesocriconema onoense (Tylenchida: Criconematidae) from Vietnam highly suggests the synonymization of Mesocriconema brevistylus and related species. INFECTION GENETICS AND EVOLUTION 2021; 95:105090. [PMID: 34562625 DOI: 10.1016/j.meegid.2021.105090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
The genus Mesocriconema is one of the most diverse genera within the family Criconematidae, known as ring nematodes, with more than 90 species. Although species in this genus usually show distinct morphological characterizations, the identification based only on morphology can lead to misidentification in many studies resulted in a number of synonymizations in the genus over time. In this study, an integrated approach has been applied in characterizing Mesocriconema onoense from Vietnam. The molecular data of 28S rRNA, ITS, 18S rRNA regions were analyzed and discussed to confirm the correct names on GenBank. Besides, phylogenetic analyses of 28S rRNA, ITS, and 18S rRNA regions of Mesocriconema species revealed that Mesocriconema brevistylus should be considered as a junior synonym of M. onoense. Consequently, M. helicus, M. onostris, and M. paronostris should also be considered as the synonyms of M. onoense.
Collapse
Affiliation(s)
- Huu Tien Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam; Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| | - Thi Duyen Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam.
| | - Thi Mai Linh Le
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam.
| | - Quang Phap Trinh
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, 100000 Hanoi, Viet Nam.
| |
Collapse
|
12
|
Kantor MR, Handoo ZA, Subbotin SA, Bauchan GR, Mowery JD. Morphological and molecular characterization of Paratylenchus beltsvillensis n. sp. (Tylenchida: Paratylenchidae) from the rhizosphere of pine tree ( Pinus virginiana Mill) in Maryland, USA. J Nematol 2021; 53:e2021-79. [PMID: 34541548 PMCID: PMC8425311 DOI: 10.21307/jofnem-2021-079] [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: 03/18/2021] [Indexed: 11/11/2022] Open
Abstract
The pin nematode, Paratylechus beltsvillensis n. sp. collected from rhizosphere soil of a Virginia pine tree (Pinus virginiana Mill) growing in Little Paint Branch Park, Beltsville, Prince George’s County, Maryland, USA, is described and illustrated along with light and scanning electron photomicrographs. Females, males, and juveniles of this new species were recovered from soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Morphologically, females are short, body length ranging from 245 to 267 μm, stylet from 70 to 75 μm long with anchor shaped knobs, vulva located at 70–73% and small vulval flap, spermatheca large, and ovoid filled with sperms. Lateral field with three incisures, of which the outer two are prominent. Tail slender, having a rounded tail terminus. Males without stylet and have a degenerated pharynx, spicules = 17–20 µm and gubernaculum = 5.0–5.5 µm. Both morphological observations and molecular analysis of ITS and partial 28S ribosomal RNA gene sequences indicated that the specimens collected from the soil at Beltsville Park from rhizosphere soil samples from Virginia pine represents a new pin nematode species.
Collapse
Affiliation(s)
- Mihail R Kantor
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, 20705
| | - Zafar A Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, 20705
| | - Sergei A Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA, 95832.,Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Gary R Bauchan
- Electron and Confocal Microscopy, USDA, ARS, Northeast Area, Beltsville, MD, 20705
| | - Joseph D Mowery
- Electron and Confocal Microscopy, USDA, ARS, Northeast Area, Beltsville, MD, 20705
| |
Collapse
|
13
|
Clavero-Camacho I, Cantalapiedra-Navarrete C, Archidona-Yuste A, Castillo P, Palomares-Rius JE. Remarkable Cryptic Diversity of Paratylenchus spp. (Nematoda: Tylenchulidae) in Spain. Animals (Basel) 2021; 11:ani11041161. [PMID: 33919566 PMCID: PMC8073821 DOI: 10.3390/ani11041161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/05/2023] Open
Abstract
In previous studies, fifteen species of Paratylenchus, commonly known as pin nematodes, have been reported in Spain. These plant-parasitic nematodes are ectoparasites with a wide host range and global distribution. In this research, 27 populations from twelve Paratylenchus species from 18 municipalities in Spain were studied using morphological, morphometrical and molecular data. This integrative taxonomic approach allowed the identification of twelve species, four of them were considered new undescribed species and eight were already known described. The new species described here are P. caravaquenus sp. nov., P. indalus sp. nov., P. pedrami sp. nov. and P. zurgenerus sp. nov. As for the already known described species, five were considered as first reports for the country, specifically P.enigmaticus, P. hamatus, P. holdemani, P. israelensis, and P. veruculatus, while P. baldaccii, P. goodeyi and P. tenuicaudatus had already been recorded in Spain. This study provides detail morphological and molecular data, including the D2-D3 expansion segments of 28S rRNA, ITS rRNA, and partial mitochondrial COI regions for the identification of different Paratylenchus species found in Spain. These results confirm the extraordinary cryptic diversity in Spain and with examples of morphostatic speciation within the genus Paratylenchus.
Collapse
Affiliation(s)
- Ilenia Clavero-Camacho
- Campus de Excelencia Internacional Agroalimentario, ceiA3, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain; (I.C.-C.); (C.C.-N.); (P.C.)
| | - Carolina Cantalapiedra-Navarrete
- Campus de Excelencia Internacional Agroalimentario, ceiA3, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain; (I.C.-C.); (C.C.-N.); (P.C.)
| | - Antonio Archidona-Yuste
- Centro Alameda del Obispo, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), 14004 Córdoba, Spain;
- Helmholtz Centre for Environmental Research-FZ, Department of Ecological Modelling, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Pablo Castillo
- Campus de Excelencia Internacional Agroalimentario, ceiA3, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain; (I.C.-C.); (C.C.-N.); (P.C.)
| | - Juan Emilio Palomares-Rius
- Campus de Excelencia Internacional Agroalimentario, ceiA3, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain; (I.C.-C.); (C.C.-N.); (P.C.)
- Correspondence:
| |
Collapse
|
14
|
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.
Collapse
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.)
| |
Collapse
|
15
|
Azimi S, Abolafia J, Pedram M. Hemicycliophora ahvasiensis n. sp. (Nematoda: Hemicycliophoridae), and data on a known species, from Iran. J Nematol 2021; 52:e2020-128. [PMID: 33829170 PMCID: PMC8015286 DOI: 10.21307/jofnem-2020-128] [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: 08/24/2020] [Indexed: 11/20/2022] Open
Abstract
Hemicycliophora ahvasiensis n. sp., recovered from the rhizospheric soil of date palm in Khuzestan province, southwest Iran, is described and illustrated based upon morphological, morphometric and molecular data. The new species is characterized by its sheath, closely fitting most of the body, cuticle with or without numerous irregular lines, sometimes appearing as blocks in distal body region. Lateral field without discrete longitudinal lines, but often with continuous broken striae or anastomoses. Continuous lip region with single annulus, slightly elevated labial disc, stylet with posteriorly sloping knobs. Vulva with or without slightly modified lips, spermatheca with sperm and tail conoid, symmetrically narrowing at distal region to form a narrow conical region. Morphologically, the new species looks similar to H. indica, H. labiata, H. siddiqii, H. tenuistriata and H. typica. The latter species appears more similar to the new species under light microscopy, but could be separated using the scanning electron microscopy and molecular data. The new species was also compared with H. epicharoides and H. dulli, two species with close phylogenetic affinities to it. The phylogenetic relationships of the new species were reconstructed and discussed using partial sequences of the D2-D3 expansion segments of large subunit, and internal transcribed spacer regions (LSU D2-D3 and ITS rDNA). Hemicycliophora conida, the second studied species, was recovered from north Iran and characterized by morphological and molecular data.
Collapse
Affiliation(s)
- Sedighe Azimi
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus de las Lagunillas, Avenida de Ben Saprut s/n. 23071-Jaén, Spain
| | - Majid Pedram
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
16
|
Flis Ł, Kornobis FW, Kubicz M, Guðmundsson J. New records of plant-parasitic nematodes from Iceland. Polar Biol 2020. [DOI: 10.1007/s00300-020-02732-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractThe plant-parasitic nematodes of Iceland are poorly understood. To address this, a study of the nematodes of the families Criconematidae and Hemicycliophoridae was performed in 2015. Soil samples were taken from underneath various host plants in different locations in Iceland. The identification was performed on the basis of the general morphology and subsequently confirmed by molecular markers (D2-D3 28S rDNA). The study revealed the presence of nematode specimens belonging to four species of the family Criconematidae: Criconemoides amorphus, Criconema demani, Mesocriconema xenoplax and Mesocriconema curvatum, as well as one species Hemicycliophora conida of the family Hemicycliophoridae. To our knowledge, this is the first record of the occurrence of these nematode species in Iceland. The species identified are economically important plant-parasitic nematodes of likely interest to—among others—Icelandic plant protection professionals. This report broadens our knowledge of Iceland’s nematode biodiversity; moreover, morphological analyses and molecular data may contribute to better understanding the origin of nematode species on the island of Iceland.
Collapse
|
17
|
Powers TO, Harris TS, Higgins RS, Mullin PG, Powers KS. Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea. Genome 2020; 64:232-241. [PMID: 32526150 DOI: 10.1139/gen-2019-0196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nematodes are frequently cited as underrepresented in faunistic surveys using DNA barcoding with COI. This underrepresentation is generally attributed to a limited presence of nematodes in DNA databases which, in turn, is often ascribed to structural variability and high evolutionary rates in nematode mitochondrial genomes. Empirical evidence, however, indicates that many taxa are readily amplified with primer sets specifically targeted to different nematode families. Here we report the development of a COI reference library of 1726 specimens in the terrestrial plant parasitic nematode superfamily Criconematoidea. Specimens collected during an ecoregion survey of North America were individually photographed, measured, and PCR amplified to produce a 721 bp region of COI for taxonomic analysis. A neighbor-joining tree structured the dataset into 179 haplotype groups that generally conformed to morphospecies in traditional analysis or Barcode Index Numbers (BINs) in the BOLD system, although absent formal BIN membership due to insufficient overlap with the Folmer region of COI. Approximately one-third of the haplotype groups could be associated with previously described species. The geographic distribution of criconematid nematode species suggests a structure influenced by the major habitat types in the United States and Canada. All sequences collected in the ecoregion survey are deposited in BOLD.
Collapse
Affiliation(s)
- Thomas O Powers
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Timothy S Harris
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca S Higgins
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peter G Mullin
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kirsten S Powers
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
18
|
|
19
|
Ahmed M, Back MA, Prior T, Karssen G, Lawson R, Adams I, Sapp M. Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.36408] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
For many organisms, there is agreement on the specific genomic region used for developing barcode markers. With nematodes, however, it has been found that the COI region designated for most animals lacks the taxonomic coverage (ability to amplify a diverse group of taxa) required of a metabarcoding marker. For that reason, studies on metabarcoding of nematodes thus far have utilized primarily regions within the highly conserved 18S ribosomal DNA. Two popular markers within this region are the ones flanked by the primer pairs NF1-18Sr2b and SSUF04-SSUR22. The NF1-18Sr2b primer pair, especially, has been critiqued as not being specific enough for nematodes leading to suggestions for other candidate markers while the SSUF04-SSUR22 region has hardly been tested on soil nematodes. The current study aimed to evaluate these two markers against other alternative ones within the 28S rDNA and the COI region for their suitability for nematode metabarcoding. The results showed that the NF1-18Sr2b marker could offer wide coverage and good resolution for characterizing soil nematodes. Sufficient availability of reference sequences for this region was found to be a significant factor that resulted in this marker outperforming the other markers, particularly the 18S-based SSUFO4-SSUR22 marker. None of the other tested regions compared with this marker in terms of the proportion of the taxa recovered. The COI-based marker had the lowest number of taxa recovered, and this was due to the poor performance of its primers and the insufficient number of reference sequences in public databases. In summary, this study highlights how dependent the success of metabarcoding is on the availability of a good reference sequence collection for the marker of choice as well as its taxonomic coverage.
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Inácio ML, Rusinque LC, Camacho MJ, Nóbrega F. First report of Mesocriconema xenoplax (Nematoda: Criconematidae) from turfgrass in Portugal and in Europe. J Nematol 2019; 51:1-6. [PMID: 31339252 PMCID: PMC6916144 DOI: 10.21307/jofnem-2019-035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 11/26/2022] Open
Abstract
In Winter 2016, root and soil samples were collected from the rhizosphere soil at 10 to 15 cm depth of turfgrass, in the yard of a complex of houses in Caxias, a region near Lisbon, Portugal. The grass (dominated by tall fescue) showed yellow patches, stunting, and poor growth. Several specimens of a ring nematode (50-60 nematodes/100 ml soil) were recovered from soil and identified as Mesocriconema xenoplax (peach ring nematode) based on morphological and morphometrical analysis of females. The observed morphological features were with previous descriptions. Species identification was confirmed through sequencing of the fragment spanning D2/D3 domain of the 28S rDNA gene. Phylogenetic analysis revealed that the Portuguese isolate grouped with M. xenoplax isolates (98% similarity), supporting its identification as M. xenoplax. This is the first report of M. xenoplax from turfgrass in Portugal and in Europe contributing with additional information on the distribution of this phytoparasite.
Collapse
Affiliation(s)
- M L Inácio
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P), Quinta do Marquês , 2780-159, Oeiras , Portugal
| | - L C Rusinque
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P), Quinta do Marquês , 2780-159, Oeiras , Portugal
| | - M J Camacho
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P), Quinta do Marquês , 2780-159, Oeiras , Portugal
| | - F Nóbrega
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P), Quinta do Marquês , 2780-159, Oeiras , Portugal
| |
Collapse
|
22
|
|
23
|
Kollár J, Pinseel E, Vanormelingen P, Poulíčková A, Souffreau C, Dvořák P, Vyverman W. A polyphasic approach to the delimitation of diatom species: a case study for the genus Pinnularia (Bacillariophyta). JOURNAL OF PHYCOLOGY 2019; 55:365-379. [PMID: 30536851 DOI: 10.1111/jpy.12825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 11/07/2018] [Indexed: 05/26/2023]
Abstract
Diatoms are one of the most abundant and arguably the most species-rich group of protists. Diatom species delimitation has often been based exclusively on the recognition of morphological discontinuities without investigation of other lines of evidence. Even though DNA sequences and reproductive experiments have revealed several examples of (pseudo)cryptic diversity, our understanding of diatom species boundaries and diversity remains limited. The cosmopolitan pennate raphid diatom genus Pinnularia represents one of the most taxon-rich diatom genera. In this study, we focused on the delimitation of species in one of the major clades of the genus, the Pinnularia subgibba group, based on 105 strains from a worldwide origin. We compared genetic distances between the sequences of seven molecular markers and selected the most variable pair, the mitochondrial cox1 and nuclear encoded LSU rDNA, to formulate a primary hypothesis on the species limits using three single-locus automated species delimitation methods. We compared the DNA-based primary hypotheses with morphology and with other available lines of evidence. The results indicate that our data set comprised 15 species of the P. subgibba group. The vast majority of these taxa have an uncertain taxonomic identity, suggesting that several may be unknown to science and/or members of (pseudo)cryptic species complexes within the P. subgibba group.
Collapse
Affiliation(s)
- Jan Kollár
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Eveline Pinseel
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Faculty of Science, Ghent University, Krijgslaan 281 - S8, 9000, Gent, Belgium
- Department of Bryophyta and Thallophyta, Botanic Garden Meise, Nieuwelaan 38, 1860, Meise, Belgium
- Ecosystem Management Research Group (ECOBE), Department of Biology, Faculty of Science, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Faculty of Science, Ghent University, Krijgslaan 281 - S8, 9000, Gent, Belgium
| | - Aloisie Poulíčková
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology and Evolutionary Biology, University of Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Faculty of Science, Ghent University, Krijgslaan 281 - S8, 9000, Gent, Belgium
| |
Collapse
|
24
|
Maria M, Cai R, Castillo P, Cantalapiedra-Navarrete C, Zheng J. Characterisation of two Chinese native Hemicriconemoides species (Nematoda: Criconematidae) with updated descriptions of H. chitwoodi Esser, 1960 and Criconemoides myungsugae Choi & Geraert, 1975. NEMATOLOGY 2019. [DOI: 10.1163/15685411-00003206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Populations of Hemicriconemoides chitwoodi, H. fujianensis, H. parasinensis, and Criconemoides myungsugae isolated in China from the rhizosphere soil of woody perennials were characterised molecularly, important morphological details being elucidated by SEM observations. The morphometric data of the Chinese populations were compared with all previously reported populations. The SEM observations of en face views indicated that H. chitwoodi and H. parasinensis have lip patterns belonging to type 1 and phylogenetically both species clustered with other Hemicriconemoides species that showed the same kind of lip pattern. On the other hand, H. fujianensis showed a lip pattern belonging to type 2 and phylogenetically appears basal to the above-mentioned clade. SEM observation of C. myungsugae showed that the first lip annulus forms a non-projecting uninterrupted disc and the labial annulus is a rectangular shape with slight dorsal and ventral indentations. Phylogenetic relationships among Criconemoides spp. are apparently not well resolved. The present study provides updated morphological descriptions, molecular diagnostics and phylogenetic relationships of H. chitwoodi, H. fujianensis, H. parasinensis, and C. myungsugae, the last species being the first report from China.
Collapse
Affiliation(s)
- Munawar Maria
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China
| | - Ruihang Cai
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China
| | - Pablo Castillo
- 2Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Carolina Cantalapiedra-Navarrete
- 2Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jingwu Zheng
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China
- 3Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, P.R. China
| |
Collapse
|
25
|
Molecular and morphological variation of the root-lesion nematode Pratylenchus neglectus. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-00165-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Barrantes-Infante BL, Schroeder BK, Subbotin SA, Murray TD. Afrina sporoboliae sp. n. (Nematoda: Anguinidae) Associated with Sporobolus cryptandrus from Idaho, United States: Phylogenetic Relationships and Population Structure. PHYTOPATHOLOGY 2018; 108:768-779. [PMID: 29327647 DOI: 10.1094/phyto-12-17-0395-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The dropseed gall-forming nematode, Afrina sporoboliae sp. n., is described from seed galls of Sporobolus cryptandrus (Poaceae: Chloridoideae: Sporobolinae) collected in Idaho, USA. This is the third report of an Afrina species in North America and the first report of this genus in a natural plant population on this continent. Morphological, morphometric, and molecular analyses placed this nematode in genus Afrina and demonstrated that it differs from Afrina hyparrheniae and Afrina spermophaga by having longer body and stylet lengths for females and males, and from Afrina wevelli by the absence of tip irregularities on the tails of female and presence of lips noticeably protruding beyond the body contour. The new species has several characters that overlap with Afrina tumefaciens, but differs from this species by inducing seed galls, whereas Afrina tumefaciens induces ovoid galls on stems, leaves, and in flower heads. Evolutionary relationships of Afrina sporoboliae sp. n. with other representatives of the family Anguinidae are presented based on analysis of the internal transcribed spacer (ITS)1-5.8S-ITS2 rRNA and the D2-D3 regions of the rRNA genes. Analysis of 270 sequences of the cox1 gene from 25 populations of Afrina sporoboliae sp. n. revealed seven haplotypes with sequence divergence up to 5%. This study did not demonstrate a significant positive relationship between genetic difference and geographic distance. Seed gall nematodes are important quarantine pests in many countries. The association of this and other seed gall nematodes with Rathayibacter species and their ability to serve as vectors, especially of R. toxicus, is of concern for U.S. agriculture.
Collapse
Affiliation(s)
- Bianca L Barrantes-Infante
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Brenda K Schroeder
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Sergei A Subbotin
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Timothy D Murray
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| |
Collapse
|
27
|
Zhuo K, Liu X, Tao Y, Wang H, Lin B, Liao J. Morphological and molecular characterisation of three species of Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) from China, with a first description of the male P. rostrocaudatus. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
In a recent survey of plant-parasitic nematodes associated with forest in China, three species of Paratylenchus, including P. aculentus, P. leptos and P. rostrocaudatus, were found. Paratylenchus leptos and P. rostrocaudatus are new records for China and the male of P. rostrocaudatus is described for the first time. Morphological descriptions, morphometrics and light microscopic photos are provided for these three species. Molecular characterisation of these species using ribosomal RNA (rRNA) D2-D3 expansion domains of large subunit (LSU D2-D3), internal transcribed spacer (ITS) and small subunit (SSU) sequences are also given. Except for the ITS sequence of P. aculentus, other sequences were amplified for the first time. Phylogenetic relationships within the genus Paratylenchus are discussed as inferred from the analyses of LSU D2-D3, ITS and SSU.
Collapse
Affiliation(s)
- Kan Zhuo
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 2Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Xingtong Liu
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 2Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Ye Tao
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 2Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Honghong Wang
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 3Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, P.R. China
| | - Borong Lin
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 2Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Jinling Liao
- 1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- 2Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
- 3Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, P.R. China
| |
Collapse
|
28
|
Van den Berg E, Tiedt L, Liébanas G, Chitambar J, Stanley J, Inserra RN, Castillo P, Subbotin S. Morphological and molecular characterisation of two new Hemicycliophora species (Tylenchida: Hemicycliophoridae) with a revision of the taxonomic status of some known species and a phylogeny of the genus. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Hemicycliophora presently contains 132 valid species of sheath nematodes. Within several samples obtained from surveys in Canada, South Africa, Spain and the USA, we distinguished six valid and six putative unidentified species by integrating the results of morphological and molecular analyses. Valid species included: H. californica, H. gracilis, H. parvana, H. poranga, H. raskii, and H. signata. The putative unidentified species were indicated as Hemicycliophora sp. 10, sp. 12, sp. 15, sp. 16, sp. 17, and sp. 18. Two new species of sheath nematodes from Spain and the USA were described and named as H. onubensis sp. n. and H. robbinsi sp. n., respectively. Hemicycliophora wyei is proposed as a junior synonym of H. parvana and H. ripa is proposed as a junior synonym of H. poranga. Eighteen valid and 13 unidentified species of sheath nematodes were characterised using the partial COI mtDNA gene. A total of 94 new sequences of which 77 were for the COI mtDNA gene were obtained in this study. Phylogenetic relationships within Hemicycliophora, using the D2-D3 expansion segments of 28S rDNA, ITS rRNA and COI gene sequences, are presented as inferred from Bayesian analysis.
Collapse
Affiliation(s)
- Esther Van den Berg
- 1National Collection of Nematodes, Biosystematics Programme, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood 0121, Pretoria, South Africa
| | - Louwrens R. Tiedt
- 2Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, Potchefstroom 2520, South Africa
| | - Gracia Liébanas
- 3Department of Animal Biology, Vegetal Biology and Ecology, University of Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain
| | - John J. Chitambar
- 4Plant Pest Diagnostic Center, California Department of Food and Agriculture, CA 95832-1448, USA
| | - Jason D. Stanley
- 5Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100, Gainesville, FL 32614-7100, USA
| | - Renato N. Inserra
- 5Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100, Gainesville, FL 32614-7100, USA
| | - Pablo Castillo
- 6Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Sergei A. Subbotin
- 4Plant Pest Diagnostic Center, California Department of Food and Agriculture, CA 95832-1448, USA
- 7Center of Parasitology, A.N Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| |
Collapse
|
29
|
Maria M, Cai R, Castillo P, Zheng J. Morphological and molecular characterisation of Hemicriconemoides paracamelliae sp. n. (Nematoda: Criconematidae) and two known species of Hemicriconemoides from China. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Sheathoid nematodes of the genus Hemicriconemoides are migratory root-ectoparasites of many crops but damage is documented for only a few species. Hemicriconemoides paracamelliae sp. n., isolated in Hangzhou, Zhejiang, China, from the rhizosphere of Cinninghamia lanceolata, is described together with H. kanayaensis and H. parataiwanensis. These three species are characterised morphologically and molecularly with important morphological details elucidated by SEM photographs. The new species can be characterised by the en face view having a dorsoventrally orientated oral disc with slit-like opening, and the labial plate being composed of two lateral semi-globular shaped projections on the lateral sides of the oral disc. This new species has the first lip annulus expanded and slightly wider than the second, stylet 83 (80-85) μm long, excretory pore located 5-6 annuli posterior to the base of the pharyngeal bulb, vulva slit-like, vulval flaps absent, spermatheca rounded to oblong-shaped, and anus located 5-8 annuli posterior to vulva. The tail is elongated, conoid, with the terminal annuli curving dorsally or ventrally to form a finely rounded tip. The study provides the first record of H. kanayaensis from mainland China, a new host association of H. parataiwanensis, and molecular sequencing data of the 18S, 28S D2-D3 and ITS sequences.
Collapse
Affiliation(s)
- Munawar Maria
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Hangzhou 310058, Zhejiang, P.R. China
| | - Ruihang Cai
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Hangzhou 310058, Zhejiang, P.R. China
| | - Pablo Castillo
- 2Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jingwu Zheng
- 1Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Hangzhou 310058, Zhejiang, P.R. China
- 3Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, P.R. China
| |
Collapse
|
30
|
Qing X, Decraemer W, Claeys M, Bert W. Molecular phylogeny ofMalenchusandFilenchus(Nematoda: Tylenchidae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Xue Qing
- Department of Biology; Nematology Research Unit; Ghent University; 9000 Ghent Belgium
| | - Wilfrida Decraemer
- Department of Biology; Nematology Research Unit; Ghent University; 9000 Ghent Belgium
| | - Myriam Claeys
- Department of Biology; Nematology Research Unit; Ghent University; 9000 Ghent Belgium
| | - Wim Bert
- Department of Biology; Nematology Research Unit; Ghent University; 9000 Ghent Belgium
| |
Collapse
|
31
|
Ghaderi R, Hamzehzarghani H, Karegar A. Numerical Taxonomy Helps Identification of Merliniidae and Telotylenchidae (Nematoda: Tylenchoidea) from Iran. J Nematol 2017; 49:207-222. [PMID: 28706320 DOI: 10.21307/jofnem-2017-065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Numerical taxonomy was used for identification and grouping of the genera, species, and populations in the families Merliniidae and Telotylenchidae. The variability of each of 44 morphometric characters was evaluated by calculation of the coefficient of variability (CV) and the ratio of extremes (max/min) in the range of 1,020 measured females. Also correlation and regression analyses were made between characters to find potential collinearities. Hierarchical cluster analysis (HCA) was used for (i) grouping 21 genera in the superfamily Dolichodoroidea based on literature data coded for states of 18 diagnostic characters, and (ii) for grouping Iranian populations belonging to selected genera. Furthermore, STEPDISC analysis was used for (i) grouping 11 genera of Merliniidae and Telotylenchidae based on the measurements of 35 characters from 1,007 Iranian female specimens, and (ii) grouping measured females of eight species of Amplimerlinius and Pratylenchoides. The multivariate data analysis approach showed robust enough to summarize relationship between morphometric characters and group genera, species, and populations of the nematodes and in particular help to identify the genera and species of Amplimerlinius and Pratylenchoides.
Collapse
Affiliation(s)
- Reza Ghaderi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | | | - Akbar Karegar
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| |
Collapse
|
32
|
POWERS THOMAS, HARRIS TIMOTHY, HIGGINS REBECCA, MULLIN PETER, POWERS KIRSTEN. An 18S rDNA Perspective on the Classification of Criconematoidea. J Nematol 2017. [DOI: 10.21307/jofnem-2017-069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
33
|
Pereira TJ, Baldwin JG. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation. Mol Phylogenet Evol 2016; 98:244-60. [PMID: 26926945 DOI: 10.1016/j.ympev.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/20/2016] [Accepted: 02/20/2016] [Indexed: 01/05/2023]
Abstract
Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.
Collapse
Affiliation(s)
- Tiago José Pereira
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| | - James Gordon Baldwin
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| |
Collapse
|
34
|
Xu CL, Zhao CB, Ding S, Zhang JF, Xie H. A modified crude DNA preparation for direct PCR reaction of single plant-parasitic nematodes. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Chun-Ling Xu
- Laboratory of Plant Nematology/Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Chuan-Bo Zhao
- Laboratory of Plant Nematology/Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Sha Ding
- Laboratory of Plant Nematology/Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Jian-Feng Zhang
- Laboratory of Plant Nematology/Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Hui Xie
- Laboratory of Plant Nematology/Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, P.R. China
| |
Collapse
|
35
|
Esmaeili M, Heydari R, Castillo P, Ziaie Bidhendi M, Palomares-Rius J. Molecular characterisation of two known species of Paratylenchus Micoletzky, 1922 from Iran with notes on the validity of Paratylenchus audriellus Brown, 1959. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002979] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During a survey on pin nematodes in western Iran, two populations of Paratylenchus audriellus and Paratylenchus tenuicaudatus were collected and subsequently analysed morphologically and molecularly. Paratylenchus audriellus is characterised by the long stylet (48-61 μm) and the typical female tail with a characteristic claw-like process with sharply pointed terminus. To our knowledge, the Iranian population of P. tenuicaudatus is the first record from Iran. The molecular characterisation of P. audriellus nematodes using the D2-D3 of 28S rRNA and the partial 18S rRNA gene sequences revealed that this species is clearly separated from P. straeleni and should be considered as a valid taxon.
Collapse
Affiliation(s)
- Mehrab Esmaeili
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ramin Heydari
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | | | - Juan E. Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| |
Collapse
|
36
|
Distribution, morphology, seasonal dynamics, and molecular characterization of Tylenchulus semipenetrans from citrus orchards in southern Iran. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
37
|
Zeng Y, Ye W, Kerns J, Tredway L, Martin S, Martin M. Molecular Characterization and Phylogenetic Relationships of Plant-Parasitic Nematodes Associated with Turfgrasses in North Carolina and South Carolina, United States. PLANT DISEASE 2015; 99:982-993. [PMID: 30690976 DOI: 10.1094/pdis-10-14-1060-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The near-full-length 18S ribosomal DNA (rDNA) gene and internal transcribed spacer 1 region were amplified and sequenced from 52 nematode populations belonging to 28 representative species in 13 families recovered from turfgrasses in North Carolina (38 populations) and South Carolina (14 populations). This study also included 13 nematode populations from eight other plant hosts from North Carolina for comparison. Nematodes were molecularly characterized and the phylogenetic relationships were explored based on 18S rDNA sequences. Phylogenetic analysis using Bayesian inference was performed using five groups of the plant-parasitic nematode populations Tylenchids, Criconematids, Longidorids, Xiphinematids, and Trichodorids. The 65 nematode populations were clustered correspondingly within appropriate positions of 13 families, including Belonolaimidae, Caloosiidae, Criconematidae, Dolichodoridae, Hemicycliophoridae, Hoplolaimidae, Heteroderidae, Longidoridae, Meloidogynidae, Paratylenchidae, Pratylenchidae, Telotylenchidae, and Trichodoridae. This study confirms previous morphological-based identification of the plant-parasitic nematode species found in turfgrasses and provides a framework for future studies of plant-parasitic nematodes associated with turfgrasses based upon DNA sequences and phylogenetic relationships.
Collapse
Affiliation(s)
- Yongsan Zeng
- Department of Plant Protection, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China; Department of Plant Pathology, North Carolina State University, Raleigh 27695
| | - Weimin Ye
- Nematode Assay Section, Agronomic Division, North Carolina Department of Agriculture and Consumer Services, Raleigh 27607
| | - James Kerns
- Department of Plant Pathology, North Carolina State University, Raleigh
| | - Lane Tredway
- Department of Plant Pathology, North Carolina State University, Raleigh
| | - Samuel Martin
- School of Agricultural, Forest and Environmental Sciences, Pee Dee Research & Education Center, Florence, SC 29506
| | - Matt Martin
- Crop Science Department, North Carolina State University, Castle Hayne 28429
| |
Collapse
|
38
|
Van den Berg E, Tiedt LR, Inserra RN, Stanley JD, Vovlas N, Palomares-Rius JE, Castillo P, Subbotin SA. Characterisation of a topotype and other populations of Hemicriconemoides strictathecatus Esser, 1960 (Nematoda: Criconematidae) from Florida with description of H. phoenicis sp. n. from the USA. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002866] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The results of morphological and molecular analyses of a Florida topotype and other populations of Hemicriconemoides strictathecatus showed that this sheathoid nematode consists of two morphotypes, both with an average stylet length of more than 70 μm, but having different tail termini, bluntly pointed or rounded. These findings confirmed the morphological similarity of H. strictathecatus with H. mangiferae, which was considered a junior synonym of this species as previously proposed by Decraemer & Geraert (1992, 1996). Populations of a sheathoid nematode with a stylet length ranging from 62.5 to 72.0 μm from Taiwan, China, South Africa and Venezuela and identified in previous studies as H. strictathecatus were found to be morphologically and molecularly different from this species and are now considered as representatives of H. litchi. Another sheathoid nematode population from Florida, considered to be H. mangiferae by McSorley et al. (1980), was also found to be morphologically and molecularly congruous with H. litchi. During nematological surveys in Florida, a new sheathoid nematode was detected on date palms imported from California into Florida and is described herein as H. phoenicis sp. n. This new species is related morphologically to the H. strictathecatus morphotype with pointed tail terminus. Both have a stylet longer than 70 μm. The new species is phylogenetically related to H. strictathecatus and H. litchi. It differs morphologically from other Hemicriconemoides species by the cuticular ornamentation of the annuli, which are marked by coarse longitudinal ridges, grooves and thick margins. Morphological and molecular characterisations of H. cocophillus from Mozambique and Florida, USA are also elucidated in this study. New phylogenies of the genus Hemicriconemoides as inferred from the analyses of the ITS rRNA, D2-D3 of 28S rRNA and partial coxI gene sequences are provided.
Collapse
Affiliation(s)
- Esther Van den Berg
- National Collection of Nematodes, Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood 0121, South Africa
| | - Louwrens R. Tiedt
- Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, Potchefstroom 2520, South Africa
| | - Renato N. Inserra
- Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100 Gainesville, FL 32614-7100, USA
| | - Jason D. Stanley
- Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100 Gainesville, FL 32614-7100, USA
| | - Nicola Vovlas
- Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (C.N.R.), U.O.S. di Bari, Via G. Amendola 122D, 70126 Bari, Italy
| | - Juan E. Palomares-Rius
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Apdo. 4084, 14080 Córdoba, Spain
| | - Pablo Castillo
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Apdo. 4084, 14080 Córdoba, Spain
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| |
Collapse
|
39
|
Subbotin SA, Chitambar JJ, Chizhov VN, Stanley JD, Inserra RN, Doucet ME, McClure M, Ye W, Yeates GW, Mollov DS, Cantalapiedra-Navarrete C, Vovlas N, Van Den Berg E, Castillo P. Molecular phylogeny, diagnostics, and diversity of plant-parasitic nematodes of the genusHemicycliophora(Nematoda: Hemicycliophoridae). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergei A. Subbotin
- Plant Pest Diagnostic Center; California Department of Food and Agriculture; 3294 Meadowview Road Sacramento CA 95832-1448 USA
- Center of Parasitology of A.N. Severtsov; Institute of Ecology and Evolution of the Russian Academy of Sciences; Leninskii Prospect 33 Moscow 117071 Russia
| | - John J. Chitambar
- Plant Pest Diagnostic Center; California Department of Food and Agriculture; 3294 Meadowview Road Sacramento CA 95832-1448 USA
| | - Vlamidir N. Chizhov
- Center of Parasitology of A.N. Severtsov; Institute of Ecology and Evolution of the Russian Academy of Sciences; Leninskii Prospect 33 Moscow 117071 Russia
| | - Jason D. Stanley
- Florida Department of Agriculture and Consumer Services; DPI; Nematology Section; P.O. Box 147100 Gainesville FL 32614-7100 USA
| | - Renato N. Inserra
- Florida Department of Agriculture and Consumer Services; DPI; Nematology Section; P.O. Box 147100 Gainesville FL 32614-7100 USA
| | - Marcelo E. Doucet
- Centro de Zoología Aplicada; Facultad de Ciencias Exactas; Físicas y Naturales; Facultad de Ciencias Agropecuarias; Universidad Nacional de Córdoba; Argentina
| | - Michael McClure
- School of Plant Sciences; University of Arizona; Tucson AZ 85721 USA
| | - Weimin Ye
- Nematode Assay Section; Agronomic Division; North Carolina Department of Agriculture & Consumer Services; 1040 Mail Service Center Raleigh NC 27699-1040 USA
| | | | - Dimitre S. Mollov
- Department of Plant Pathology; University of Minnesota; St. Paul MN 55108 USA
| | - Carolina Cantalapiedra-Navarrete
- Instituto de Agricultura Sostenible (IAS); Consejo Superior de Investigaciones Científicas (CSIC); Campus de Excelencia Internacional Agroalimentario; ceiA3, Apdo. 4084 14080 Córdoba Spain
| | - Nicola Vovlas
- Istituto per la Protezione delle Piante (IPP); Sezione di Bari; Consiglio Nazionale delle Ricerche, (C.N.R.); Via G. Amendola 165/A 70126 Bari Italy
| | - Esther Van Den Berg
- National Collection of Nematodes; Biosystematics Programme; ARC-Plant Protection Research Institute; Private Bag X134 Queenswood 0121 South Africa
| | - Pablo Castillo
- Instituto de Agricultura Sostenible (IAS); Consejo Superior de Investigaciones Científicas (CSIC); Campus de Excelencia Internacional Agroalimentario; ceiA3, Apdo. 4084 14080 Córdoba Spain
| |
Collapse
|
40
|
Koshel EI, Aleshin VV, Eroshenko GA, Kutyrev VV. Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague. BIOMED RESEARCH INTERNATIONAL 2014; 2014:135218. [PMID: 24804197 PMCID: PMC3996313 DOI: 10.1155/2014/135218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/05/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.
Collapse
Affiliation(s)
- E. I. Koshel
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Aleshin
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- National Research Institute of Physiology, Biochemistry, and Nutrition of Farm Animals, Russian Academy of Agricultural Sciences, Kaluga Region, Borovsk 249013, Russia
| | - G. A. Eroshenko
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Kutyrev
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| |
Collapse
|
41
|
Van den Berg E, Tiedt LR, Inserra R, Stanley J, Vovlas N, Palomares Rius J, Castillo P, Subbotin S. Morphological and molecular characterisation of some Hemicriconemoides species (Nematoda: Criconematidae) together with a phylogeny of the genus. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002786] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sheathoid nematodes of the genusHemicriconemoidesare migratory root-ectoparasites of many plants including various agricultural crops and fruit trees. They are generally found inhabiting warm areas of the world and presently consist of 52 valid species. In this study we provide morphological and molecular characterisation of 12 species of this genusviz.:H. alexis,H. brachyurus,H. californianus,H. chitwoodi,H. macrodorus,H. minutus,H. ortonwilliamsi,H. promissus,H. silvaticus,H. strictathecatus,H. wessoniandHemicriconemoidessp. originating from China, Greece, Japan, Myanmar, Spain, South Africa and the USA. Morphological descriptions, measurements, light and scanning electron microscopic observations and drawings are given for several species. Phylogenetic relationships withinHemicriconemoides, as inferred from the analyses of the D2-D3 of 28S rRNA and ITS-rRNA gene sequences, resulted in trees with three major clades that corresponded with species groupings based on morphology of the lip pattern and vulval flap. PCR with species-specific primers were developed forH. californianus,H. chitwoodiandH. strictathecatus.
Collapse
Affiliation(s)
- Esther Van den Berg
- National Collection of Nematodes, Biosystematics Programme, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood 0121, South Africa
| | - Louwrens R. Tiedt
- Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, Potchefstroom 2520, South Africa
| | - Renato N. Inserra
- Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100 Gainesville, FL 32614-7100, USA
| | - Jason D. Stanley
- Florida Department of Agriculture and Consumer Services, DPI, Nematology Section, P.O. Box 147100 Gainesville, FL 32614-7100, USA
| | - Nicola Vovlas
- Istituto per la Protezione delle Piante (IPP), Sezione di Bari, Consiglio Nazionale delle Ricerche (CNR), Via G. Amendola 122D, 70126 Bari, Italy
| | - Juan E. Palomares Rius
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Apdo. 4084, 14080 Córdoba, Spain
| | - Pablo Castillo
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Apdo. 4084, 14080 Córdoba, Spain
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| |
Collapse
|
42
|
Van den Berg E, Van den Berg E, Tiedt LR, Van den Berg E, Tiedt LR, Subbotin SA. Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002769] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.
Collapse
Affiliation(s)
- Esther Van den Berg
- 1Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood, 0121 Pretoria, South Africa
| | - Esther Van den Berg
- 1Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood, 0121 Pretoria, South Africa
| | - Louwrens R. Tiedt
- 2Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, 2520 Potchefstroom, South Africa
| | - Esther Van den Berg
- 1Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood, 0121 Pretoria, South Africa
| | - Louwrens R. Tiedt
- 2Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, 2520 Potchefstroom, South Africa
| | - Sergei A. Subbotin
- 3Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- 4Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| |
Collapse
|
43
|
Shylla JA, Ghatani S, Tandon V. Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea). Parasitol Res 2013; 112:4239-53. [PMID: 24096607 DOI: 10.1007/s00436-013-3616-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/19/2013] [Indexed: 11/29/2022]
Abstract
Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.
Collapse
Affiliation(s)
- Jollin A Shylla
- Department of Zoology, North-Eastern Hill University, Shillong, 793022, Meghalaya, India
| | | | | |
Collapse
|
44
|
Ashrafi S, Mugniéry D, van Heese EY, van Aelst AC, Helder J, Karssen G. Description of Meloidoderita salina sp. n. (Nematoda, Sphaeronematidae) from a micro-tidal salt marsh at Mont-Saint-Michel Bay in France. Zookeys 2013:1-26. [PMID: 23378798 PMCID: PMC3536011 DOI: 10.3897/zookeys.249.4138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/23/2012] [Indexed: 11/30/2022] Open
Abstract
Meloidoderita salinasp. n. is described and illustrated from the halophytic plant Atriplex portulacoides L. (sea purslane) growing in a micro-tidal salt marsh in the Mont-Saint-Michel Bay in France. This new species is the first member of Meloidoderita Poghossian, 1966 collected from a saline environment, and is characterized by the following features: sedentary mature females having a small swollen body with a clear posterior protuberance; slightly dorsally curved stylet, 19.9 µm long, with posteriorly sloping knobs; neck region irregular in shape and twisted; well developed secretory-excretory (S–E) pore, with markedly sclerotized S-E duct running posteriorly; prominent uterus bordered by a thick hyaline wall and filled with eggs. The adult female transforms into a cystoid. Eggs are deposited in both egg-mass and cystoid. Cystoids of Meloidoderita salinasp.n. display a unique sub-cuticular hexagonal beaded pattern.
Male without stylet, pharyngeal region degenerated, S-E duct prominent, deirids small, developed testis 97.5 µm long, spicules 18.4 µm long, cloacal opening ventrally protruded, small phasmids posterior to cloaca opening and situated at 5.9 (3.2–7.7) µm from tail end, and conical tail ending in a rounded terminus marked with one (rarely two) ventrally positioned mucro. Additionally, some young malesof the new species were observed enveloped in the last J2 cuticle. Second-stage juvenile body 470 µm long, with a 16.4 µm long stylet, prominent rounded knobs set off from the shaft, hemizonid anterior and adjacent to S-E pore, small deirids located just above S-E pore level, genital primordium located at 68–77% of body length, phasmids small and located at about 19 µm from tail tip, and tail 38.7 µm long, tapering to finely pointed terminus with a finger-like projection. Phylogenetic analyses based on the nearly full length small subunit ribosomal DNA sequences of Meloidoderita salinasp. n. revealed a close relationship of the new species with Sphaeronema alni Turkina & Chizhov, 1986 and placed these two species sister to the rest of Criconematina.
Collapse
Affiliation(s)
- Samad Ashrafi
- Plant Protection Service, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands ; Ghent University, Department of Biology, Ledeganckstraat 35, 9000 Ghent, Belgium
| | | | | | | | | | | |
Collapse
|
45
|
Pereira TJ, Fonseca G, Mundo-Ocampo M, Guilherme BC, Rocha-Olivares A. Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy. MARINE BIOLOGY 2010; 157:1665-1678. [PMID: 24391248 PMCID: PMC3873033 DOI: 10.1007/s00227-010-1439-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.
Collapse
Affiliation(s)
- Tiago José Pereira
- />Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Apdo. Postal 2732, CP 22860 Ensenada, Baja California Mexico
- />Department of Nematology, University of California, Riverside, CA 92521 USA
| | - Gustavo Fonseca
- />Centro de Biologia Marinha da Universidade de São Paulo, Rod. Manoel Hipolito do Rego km 131.5, São Sebastião, 11600-000 Brazil
| | - Manuel Mundo-Ocampo
- />Department of Nematology, University of California, Riverside, CA 92521 USA
| | - Betânia Cristina Guilherme
- />Centro de Educação e Saúde, CES, Universidade Federal de Campina Grande, Av. Olho D’Água da Bica s/n, Cuité, PB Brazil
| | - Axayácatl Rocha-Olivares
- />Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Apdo. Postal 2732, CP 22860 Ensenada, Baja California Mexico
| |
Collapse
|
46
|
Bert W, Leliaert F, Vierstraete AR, Vanfleteren JR, Borgonie G. Molecular phylogeny of the Tylenchina and evolution of the female gonoduct (Nematoda: Rhabditida). Mol Phylogenet Evol 2008; 48:728-44. [DOI: 10.1016/j.ympev.2008.04.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 03/31/2008] [Accepted: 04/01/2008] [Indexed: 11/25/2022]
|
47
|
Subbotin SA, Ragsdale EJ, Mullens T, Roberts PA, Mundo-Ocampo M, Baldwin JG. A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Mol Phylogenet Evol 2008; 48:491-505. [PMID: 18514550 DOI: 10.1016/j.ympev.2008.04.028] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 04/14/2008] [Accepted: 04/21/2008] [Indexed: 11/26/2022]
Abstract
The root lesion nematodes of the genus Pratylenchus Filipjev, 1936 are migratory endoparasites of plant roots, considered among the most widespread and important nematode parasites in a variety of crops. We obtained gene sequences from the D2 and D3 expansion segments of 28S rRNA partial and 18S rRNA from 31 populations belonging to 11 valid and two unidentified species of root lesion nematodes and five outgroup taxa. These datasets were analyzed using maximum parsimony and Bayesian inference. The alignments were generated using the secondary structure models for these molecules and analyzed with Bayesian inference under the standard models and the complex model, considering helices under the doublet model and loops and bulges under the general time reversible model. The phylogenetic informativeness of morphological characters is tested by reconstruction of their histories on rRNA based trees using parallel parsimony and Bayesian approaches. Phylogenetic and sequence analyses of the 28S D2-D3 dataset with 145 accessions for 28 species and 18S dataset with 68 accessions for 15 species confirmed among large numbers of geographical diverse isolates that most classical morphospecies are monophyletic. Phylogenetic analyses revealed at least six distinct major clades of examined Pratylenchus species and these clades are generally congruent with those defined by characters derived from lip patterns, numbers of lip annules, and spermatheca shape. Morphological results suggest the need for sophisticated character discovery and analysis for morphology based phylogenetics in nematodes.
Collapse
Affiliation(s)
- Sergei A Subbotin
- Department of Nematology, University of California, Riverside, CA 92521, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Ye W, Giblin-Davis RM, Davies KA, Purcell MF, Scheffer SJ, Taylor GS, Center TD, Morris K, Thomas WK. Molecular phylogenetics and the evolution of host plant associations in the nematode genus Fergusobia (Tylenchida: Fergusobiinae). Mol Phylogenet Evol 2007; 45:123-41. [PMID: 17434761 DOI: 10.1016/j.ympev.2007.02.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 02/04/2007] [Accepted: 02/15/2007] [Indexed: 10/23/2022]
Abstract
Fergusobia nematodes (Tylenchida: Fergusobiinae) and Fergusonina flies (Diptera: Fergusoninidae) are putative mutualists that develop together in galls formed in meristematic tissues of many species of the plant family Myrtaceae in Australasia. Fergusobia nematodes were sampled from a variety of myrtaceous hosts and gall types from Australia and one location in New Zealand between 1999 and 2006. Evolutionary relationships of these isolates were inferred from phylogenetic analyses of the DNA sequences of the nuclear ribosomal DNA near-full length small subunit (up to 1689bp for 21 isolates), partial large subunit D2/D3 domain (up to 889bp for 87 isolates), partial mitochondrial cytochrome oxidase subunit I (618 bp for 82 isolates), and combined D2/D3 and mtCOI (up to 1497bp for 66 isolates). The SSU data supported a monophyletic Fergusobia genus within a paraphyletic Howardula. A clade of Drosophila-associated Howardula, including Howardula aoronymphium, was the closest sequenced sister group. Phylogenetic analysis of sequences from D2/D3 and mtCOI, separately and combined, revealed many monophyletic clades within Fergusobia. The relationships inferred by D2/D3 and mtCOI were congruent with some exceptions. Well-supported clades were generally consistent with host plant species and gall type. However, phylogenetic analysis suggested host switching or putative hybridization events in many groups, except the lineage of shoot bud gallers on the broad-leaved Melaleuca species complex.
Collapse
Affiliation(s)
- Weimin Ye
- Fort Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Fort Lauderdale, FL 33314, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Subbotin SA, Sturhan D, Vovlas N, Castillo P, Tambe JT, Moens M, Baldwin JG. Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934. Mol Phylogenet Evol 2006; 43:881-90. [PMID: 17101282 DOI: 10.1016/j.ympev.2006.09.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 09/25/2006] [Accepted: 09/26/2006] [Indexed: 11/24/2022]
Abstract
Knowledge of rRNA structure is increasingly important to assist phylogenetic analysis through reconstructing optimal alignment, utilizing molecule features as an additional source of data and refining appropriate models of evolution of the molecule. We describe a procedure of optimization for alignment and a new coding method for nucleotide sequence data using secondary structure models of the D2 and D3 expansion fragments of the LSU-rRNA gene reconstructed for fifteen nematode species of the agriculturally important and diverse family Hoplolaimidae, order Tylenchida. Using secondary structure information we converted the original sequence data into twenty-eight symbol codes and submitted the transformed data to maximum parsimony analysis. We also applied the original sequence data set for Bayesian inference. This used the doublet model with sixteen states of nucleotide doublets for the stem region and the standard model of DNA substitution with four nucleotide states for loops and bulges. By this approach, we demonstrate that using structural information for phylogenetic analyses led to trees with lower resolved relationships between clades and likely eliminated some artefactual support for misinterpreted relationships, such as paraphyly of Helicotylenchus or Rotylenchus. This study as well as future phylogenetic analyses is herein supported by the development of an on-line database, NEMrRNA, for rRNA molecules in a structural format for nematodes. We also have developed a new computer program, RNAstat, for calculation of nucleotide statistics designed and proposed for phylogenetic studies.
Collapse
Affiliation(s)
- Sergei A Subbotin
- Department of Nematology, University of California, Riverside, CA 92521, USA.
| | | | | | | | | | | | | |
Collapse
|