40 results on '"CASTILLO, Pablo"'
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2. Molecular and morphological characterization of the spiral nematode Helicotylenchus oleae Inserra, Vovlas & Golden, 1979 (Nematoda: Hoplolaimidae) in the Mediterranean Basin
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Palomares-Rius, Juan E., Cantalapiedra-Navarrete, Carolina, Archidona-Yuste, Antonio, Vovlas, Nicola, Tzortzakakis, Emmanuel A., and Castillo, Pablo
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- 2018
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3. A new dagger nematode, Xiphinema tica n. sp. (Nematoda: Longidoridae), from Costa Rica with updating of the polytomous key of Loof and Luc (1990)
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Peraza-Padilla, Walter, Cantalapiedra-Navarrete, Carolina, Zamora-Araya, Tatiana, Palomares-Rius, Juan E., Castillo, Pablo, and Archidona-Yuste, Antonio
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- 2018
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4. Molecular characterization of pseudomonodelphic dagger nematodes of the genus Xiphinema Cobb, 1913 (Nematoda: Longidoridae) in Costa Rica, with notes on Xiphinema setariae Tarjan, 1964
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Peraza-Padilla, Walter, Archidona-Yuste, Antonio, Ferris, Howard, Zamora-Araya, Tatiana, Cantalapiedra-Navarrete, Carolina, Palomares-Rius, Juan E., Subbotin, Sergei A., and Castillo, Pablo
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- 2017
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5. Molecular characterization and distribution of the needle nematode Longidorus laevicapitatus Williams, 1959 (Nematoda: Longidoridae) in Costa Rica
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Peraza-Padilla, Walter, Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, Zamora-Araya, Tatiana, Palomares-Rius, Juan E., and Castillo, Pablo
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- 2017
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6. Integrative identification and molecular phylogeny of dagger and needle nematodes associated with cultivated olive in Tunisia
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Guesmi-Mzoughi, Ilhem, Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, Palomares-Rius, Juan E., Regaieg, Hajer, Horrigue-Raouani, Najet, and Castillo, Pablo
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- 2017
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7. A new needle nematode, Longidorus persicus n. sp. (Nematoda: Longidoridae), from Kermanshah province, western Iran
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Esmaeili, Mehrab, Heydari, Ramin, Archidona-Yuste, Antonio, Castillo, Pablo, and Palomares-rius, Juan E.
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- 2017
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8. Root-lesion nematodes of the genus Pratylenchus (Nematoda: Pratylenchidae) from Costa Rica with molecular identification of P. gutierrezi and P. panamaensis topotypes
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Araya, Tatiana Zamora, Padilla, Walter Peraza, Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, Liébanas, Gracia, Palomares-Rius, Juan E., and Castillo, Pablo
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- 2016
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9. Description of a new needle nematode, Longidorus asiaticus n. sp. (Nematoda: Longidoridae), from the rhizosphere of crape myrtle (Lagerstroemia indica) bonsai trees imported into Italy from China
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Trisciuzzi, Nicola, Archidona-Yuste, Antonio, Troccoli, Alberto, Fanelli, Elena, De Luca, Francesca, Vovlas, Nicola, and Castillo, Pablo
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- 2015
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10. A new root-knot nematode Meloidogyne spartelensis n. sp. (Nematoda: Meloidogynidae) in Northern Morocco
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Ali, Nadine, Tavoillot, Johannes, Mateille, Thierry, Chapuis, Elodie, Besnard, Guillaume, El Bakkali, Ahmed, Cantalapiedra-Navarrete, Carolina, Liébanas, Gracia, Castillo, Pablo, and Palomares-Rius, Juan E.
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- 2015
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11. Integrative diagnosis and molecular phylogeny of dagger and needle nematodes of olives and grapevines in the island of Crete, Greece, with description of Xiphinema cretense n. sp. (Nematoda, Longidoridae)
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Tzortzakakis, Emmanuel A., Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, Nasiou, Eleni, Lazanaki, Maria S., Kabourakis, Emmanouil M., Palomares-Rius, Juan E., and Castillo, Pablo
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- 2014
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12. Morphological and molecular characterisation of Pratylenchus oleae n. sp. (Nematoda: Pratylenchidae) parasitizing wild and cultivated olives in Spain and Tunisia
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Palomares-Rius, Juan E., Guesmi, Ilhem, Horrigue-Raouani, Najet, Cantalapiedra-Navarrete, Carolina, Liébanas, Gracia, and Castillo, Pablo
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- 2014
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13. Phylogeny, diversity, and species delimitation in some species of the Xiphinema americanum-group complex (Nematoda: Longidoridae), as inferred from nuclear and mitochondrial DNA sequences and morphology
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Gutiérrez-Gutiérrez, Carlos, Cantalapiedra-Navarrete, Carolina, Decraemer, Wilfrida, Vovlas, Nicola, Prior, Tom, Rius, Juan E. Palomares, and Castillo, Pablo
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- 2012
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14. Molecular variability and phylogenetic relationships among different species and populations of Pratylenchus (Nematoda: Pratylenchidae) as inferred from the analysis of the ITS rDNA
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De Luca, Francesca, Reyes, Aurelio, Troccoli, Alberto, and Castillo, Pablo
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- 2011
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15. Prevalence, polyphasic identification, and molecular phylogeny of dagger and needle nematodes infesting vineyards in southern Spain
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Gutiérrez-Gutiérrez, Carlos, Palomares Rius, Juan E., Cantalapiedra-Navarrete, Carolina, Landa, Blanca B., and Castillo, Pablo
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- 2011
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16. New evidence of cryptic speciation in the family Longidoridae (Nematoda: Dorylaimida).
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Cai, Ruihang, Archidona‐Yuste, Antonio, Cantalapiedra‐Navarrete, Carolina, Palomares‐Rius, Juan E., and Castillo, Pablo
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GENETIC speciation ,NEMATODES ,CYTOCHROME oxidase ,PLANT nematodes - Abstract
Longidorid nematodes comprise more than 500 species, and Longidorus and Xiphinema are the most diversified, prevalent, and cosmopolitan genera within plant‐parasitic nematodes. This increases the risk of species misidentification. We conducted an integrative morphometric and genetic study on two longidorid species to elucidate the existence of new cases of cryptic speciation within the genera Longidorus and Xiphinema. Detailed morphological, morphometrical, multivariate, and genetic studies were carried out, and mitochondrial and nuclear haploweb analyses were used to differentiate species within the L. iliturgiensis and X. hispanum complexes. Species delimitation using multivariate and haplonet tools of L. iliturgiensis species complex clearly separated L. tabernensis sp. nov. from L. iliturgiensis and L. indalus, and X. subbaetense sp. nov. from X. hispanum and X. adenohystherum. D2‐D3, partial 18S, and partial coxI regions were used for inferring their phylogenetic relationships with other species in each genus. The present study provides new insights into the diversity of Longidorus and Xiphinema species detected in southern Spain, and new evidence of cryptic speciation in both genera. These results support our hypothesis that the biodiversity of Longidoridae in southern Europe is higher than previously supposed and is still not fully clarified. [ABSTRACT FROM AUTHOR]
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- 2020
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17. Integrative taxonomy unravels cryptic diversity in the Paratrichodorus hispanus -group complex and resolves two new species of the genus and the molecular phylogeny of the family (Nematoda: Trichodoridae).
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Decraemer, Wilfrida, Cantalapiedra-Navarrete, Carolina, Archidona-Yuste, Antonio, Varela-Benavides, Ingrid, Gutiérrez-Gutiérrez, Carlos, Castillo, Pablo, and Palomares-Rius, Juan E
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PLANT nematodes ,TOBRAVIRUSES ,TRICHODORUS ,RIBOSOMAL RNA - Abstract
The genus Paratrichodorus currently comprises 26 species of polyphagous ectoparasitic plant nematodes that are distributed worldwide and include a few tobravirus vector species. Paratrichodorus is one of the most difficult genera for species identification because it is phenotypically conserved, with morphometric characters that often overlap between species. From 2003 to 2016, nematode surveys were conducted in southern Spain, and the present study addresses 22 nematode populations of the Paratrichodorus hispanus group. Among them, two new species, Paratrichodorus almadenensis sp. nov. and Paratrichodorus ramblensis sp. nov. are described here morphologically and molecularly and compared with topotype specimens of Paratrichodorus hispanus. Furthermore, this analysis was complemented with the first molecular data for this species complex and for the genus Monotrichodorus. The phylogeny of family Trichodoridae showed the relationship of Monotrichodorus with Trichodorus, both of which are phylogenetically associated with the P. hispanus species group, including the two newly described species. Several phylogenetic hypotheses about the monophyly of the genera with molecular data composing the family Trichodoridae were tested using Shimodaira–Hasegawa and approximately unbiased tests. This work also includes the first observations of copulatory plugs in Paratrichodorus, which clearly differ from the different types of mating plugs described in Trichodorus species. [ABSTRACT FROM AUTHOR]
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- 2019
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18. Molecular phylogeny, diagnostics, and diversity of plant-parasitic nematodes of the genus Hemicycliophora (Nematoda: Hemicycliophoridae)
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Subbotin, Sergei A., Chitambar, John J., Chizhov, Vladimir N., Stanley, Jason D., Inserra, Renato N., Doucet, Marcelo Edmundo, Mcclure, Michael, Ye, Weimin, Yeates, George, Mollov, Dimitre S., Cantalapiedra Navarrete, Carolina, Vovlas, Nicola, Van Den Berg, Esther, and Castillo, Pablo
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Tylenchida ,cryptic species ,Nematoda ,sheath nematodes ,Bayesian inference ,D2-D3 ,rDNA ,Zoología, Ornitología, Entomología, Etología ,Biodiversity ,Secernentea ,Ciencias Biológicas ,PCR-ITS-RFLP ,Criconematidae ,Animalia ,CIENCIAS NATURALES Y EXACTAS ,ancestral state reconstructions ,Taxonomy - Abstract
The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant-parasitic nematodes, collectively known as ‘sheath nematodes’. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2-D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR-restriction fragment length polymorphisms (PCR-RFLPs) of the D2-D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2-D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira–Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far. Fil: Subbotin, Sergei A.. California Department of Food and Agriculture; Estados Unidos. Institute of Ecology and Evolution of the Russian Academy of Sciences; Rusia Fil: Chitambar, John J.. California Department of Food and Agriculture; Estados Unidos Fil: Chizhov, Vladimir N.. Institute of Ecology and Evolution of the Russian Academy of Sciences; Rusia Fil: Stanley, Jason D.. Florida Department of Agriculture and Consumer Services; Estados Unidos Fil: Inserra, Renato N.. Florida Department of Agriculture and Consumer Services; Estados Unidos Fil: Doucet, Marcelo Edmundo. Universidad Nacional de Cordoba. Facultad de Cs.exactas Fisicas y Naturales. Centro de Zoologia Aplicada; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; Argentina Fil: Mcclure, Michael. University Of Arizona; Estados Unidos Fil: Ye, Weimin. North Carolina Department of Agriculture & Consumer Services; Estados Unidos Fil: Yeates, George. Fil: Mollov, Dimitre S.. University Of Minnesota; Estados Unidos Fil: Cantalapiedra Navarrete, Carolina. Consejo Superior de Investigaciones Científicas. Instituto de Agricultura Sostenible; España Fil: Vovlas, Nicola. Istituto per la Protezione delle Piante; Italia Fil: Van Den Berg, Esther. ARC-Plant Protection Research Institute; Sudáfrica Fil: Castillo, Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Agricultura Sostenible; España
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- 2014
19. Integrative taxonomy of the stunt nematodes of the genera Bitylenchus and Tylenchorhynchus (Nematoda, Telotylenchidae) with description of two new species and a molecular phylogeny
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Handoo, Zafar A., Palomares-Rius, Juan E., Cantalapiedra-Navarrete, Carolina, Liébanas, Gracia, Subbotin, Sergei A., Castillo, Pablo, European Commission, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ministerio de Economía y Competitividad (España), Junta de Andalucía, Ministerio de Ciencia e Innovación (España), and Russian Foundation for Basic Research
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Tylenchida ,Chromadorea ,Tail tip annulation ,Nematoda ,Telotylenchidae ,Bayesian inference ,D2–D3 expansion segments of the large ribosomal subunit (28S) ,18S ,Belonolaimidae ,Biodiversity ,Shimodaira–Hasegawa test ,Secernentea ,Rhabditida ,Stylet knob inclination ,Internal transcribed spacer ,Cryptic species ,Animalia ,Taxonomy - Abstract
Stunt nematodes are characterized by phenotypic plasticity, with overlapping morphology and morphometry leading to potential misidentification. Consequently, the application of integrative taxonomic approaches is useful to species delimitation based on a combination of different perspectives, e.g. morphology and DNA sequences. We conducted nematode surveys in cultivated and natural environments in Spain and the USA, from which we identified 18 known species of the family Telotylenchidae and two new taxa within the studied samples. These species were morphologically, morphometrically, and molecularly characterized. The results of light and scanning electron microscopic observations, and molecular and phylogenetic analysis also allowed two new species to be distinguished, described herein as Bitylenchus hispaniensis sp. nov. and Tylenchorhynchus mediterraneus sp. nov. The phylogenetic analysis was carried out using molecular data from nuclear ribosomal DNA genes [D2–D3 expansion segments of the large ribosomal subunit (28S), internal transcribed spacer (ITS), and partial small ribosomal subunit (18S)]. We also provide here a test of alternative hypotheses that confirms the monophyly of both Tylenchorhynchus and Bitylenchus sensu Siddiqi's classification but does not support Fortuner & Luc's conceptual view of Tylenchorhynchus as a large genus. Ancestral state reconstructions of several diagnostic morphological characters using a maximum parsimony approach showed congruence in morphological and molecular evolution for stylet knob inclination and tail tip annulation. Our analysis emphasizes some of the problems related to the taxonomy and phylogeny of nematodes of Telotylenchinae. © 2014 The Linnean Society of London, The last author acknowledges support from grant KBBE 219262 ArimNET_ERANET FP7 2012–2015 Project PESTOLIVE ‘Contribution of olive history for the management of soilborne parasites in the Mediterranean basin’ from Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), grant AGL2012-37521 from ‘Ministerio de Economía y Competitividad’ of Spain, grants P12-AGR 1486 and AGR-136 from ‘Consejería de Economía, Innvovación y Ciencia’ from Junta de Andalucía, grant AGL2009-06955 from ‘Ministerio de Ciencia e Innovación’ of Spain, and Union Europea, Fondo Europeo de Desarrollo regional, ‘Una manera de hacer Europa’. The fifth author acknowledges the support from the Russian Foundation of Basic Research, project number 14-04-00953 A.
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- 2014
20. New insight into the identification and molecular phylogeny of dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) with description of two new species
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Gutiérrez-Gutiérrez, Carlos, Cantalapiedra-Navarrete, C., Remesal, Efrén, Palomares Rius, Juan E., Navas Cortés, Juan Antonio, Castillo, Pablo, Ministerio de Ciencia e Innovación (España), Junta de Andalucía, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), and European Commission
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Multivariate analysis ,Bayesian inference ,Cryptic species ,D2-D3 ,rDNA ,PCoA - Abstract
The genus Xiphinema constitutes a large group of about 260 species of plant-ectoparasitic nematodes. The group is polyphagous and distributed almost worldwide. Some of the species of this genus damage agricultural crops by direct feeding on root cells as well as by transmitting nepoviruses. Species discrimination in Xiphinema is complicated by phenotypic plasticity leading to potential misidentification. We conducted nematode surveys in cultivated and natural environments in Spain from 2009 to 2012, from which we identified 20 populations of Xiphinema species morphologically close to the virus-vector nematode species Xiphinema diversicaudatum, three apomictic populations tentatively identified as species from the complex Xiphinema aceri-pyrenaicum group, and one population morphologically different from all others that is characterized by a female tail elongate to conical and absence of uterine differentiation. We developed comparative multivariate analyses for these related species by using morphological and morphometrical features together with molecular data from nuclear ribosomal DNA genes [D2-D3 expansion segments of large ribosomal subunit 28S, internal transcribed spacer 1 (ITS1), and partial small ribosomal subunit (18S)]. The results of multivariate, molecular, and phylogenetic analysis confirmed the morphological hypotheses and allowed the delimitation and discrimination of two new species in the genus described herein as Xiphinema baetica sp. nov. and Xiphinema turdetanensis sp. nov., and ten known species: Xiphinema adenohystherum, Xiphinema belmontense, Xiphinema cohni, Xiphinema coxi europaeum, Xiphinema gersoni, Xiphinema hispidum, Xiphinema italiae, Xiphinema lupini, Xiphinema nuragicum, and Xiphinema turcicum. Multivariate analyses based on quantitative and qualitative characters and phylogenetic relationships of Xiphinema spp. based on the three molecular ribosomal markers resulted in a partial consensus of these species grouping as nematode populations were maintained for the majority of morphospecies groups (e.g. morphospecies groups 5 and 6), but not in some others (e.g. position of Xiphinema granatum), demonstrating the usefulness of these analyses for helping in the diagnosis and identification of Xiphinema spp. The clade topology of phylogenetic trees of D2-D3 and partial 18S regions in this study were congruent in supporting the polyphyletic status of some characters, such as the female tail shape and the degree of development of the genital system in species with both genital branches equally developed. This is the most complete phylogenetic study for Xiphinema non-americanum-group species. Agreement between phylogenetic trees and some morphological characters (uterine spines, pseudo-Z organ, and tail shape) was tested by reconstruction of their histories on rDNA-based trees using parsimony and Bayesian approaches. Thus, integrative taxonomy, based on the combination of multivariate, molecular analyses with morphology, constitutes a new insight into the identification of Xiphinema species., This research was supported by a grant AGL2009-06955 from ‘Ministerio de Ciencia e Innovación’ of Spain, grant 219262 ArimNET_ERANET FP7 2012–2015 Project PESTOLIVE ‘Contribution of olive history for the management of soilborne parasites in the Mediterranean basin’ from Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), grant AGL2012-37521 from 'Ministerio de Economía y Competitividad' of Spain, grant AGR-136 from ‘Consejería de Economía, Innvovación y Ciencia’ from Junta de Andalucía, and the European Social Fund.
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- 2013
21. Description and molecular phylogeny of one new and one known needle nematode of the genus <italic>Paralongidorus</italic> (Nematoda: Longidoridae) from grapevine in Portugal using integrative approach.
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Gutiérrez-Gutiérrez, Carlos, Mota, Manuel, Castillo, Pablo, Santos, Margarida Teixeira, and Palomares-Rius, Juan E.
- Abstract
A new and a known longidorid nematode,
Paralongidorus lusitanicus n. sp. andParalongidorus plesioepimikis , are described and illustrated from populations extracted from soil associated with grapevine (Vitis vinifera L.) from Escaroupim and Pó (central-Western Portugal), respectively. The new needle nematodeP. lusitanicus n. sp. is characterised by a very large body size (8072-12,022 μm), an expanded and rounded lip region,ca 30 μm wide, with a clear constriction followed by a depression posterior to the amphidial aperture, amphidial fovea very large (11.0-19.0 μm), stirrup-shaped, with conspicuous slit-like aperture as shown in scanning electron microscopy studies, a very long and flexible odontostyle (180.0-223.0 μm), guiding ring located at 28.0-41.5 μm from anterior end, vulva anterior to the mid-body (34-41%), a dorsally convex-conoid tail with rounded terminus (29-42 μm long), bearing two or three pairs of caudal pores and males common (ratio 1:1.6 females) with spiculesca 80 μm long. Morphological and morphometric traits forP .plesioepimikis fit well with the original description, and is reported for the first time in Portugal. Integrative diagnosis of both species was completed with molecular data obtained using D2-D3 expansion segments of 28S rDNA, ITS1-rDNA and partial 18S-rDNA. The phylogenetic relationships of these species with otherParalongidorus spp. using these three molecular markers indicated thatP. lusitanicus n. sp. clustered together with otherParalongidorus spp. forming a sister clade withP .plesioepimikis , both of them sharing a large body, long odontostyle, an anteriorly located vulva and an expanded and rounded lip region with a clear constriction followed by a depression posterior to the amphidial aperture. [ABSTRACT FROM AUTHOR]- Published
- 2018
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22. A new dagger nematode, Xiphinema poasense n. sp. (Nematoda: Longidoridae), from Costa Rica.
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VARELA-BENAVIDES, Ingrid, PERAZA-PADILLA, Walter, CANTALAPIEDRA-NAVARRETE, Carolina, PALOMARES-RIUS, Juan E., CASTILLO, Pablo, and ARCHIDONA-YUSTE, Antonio
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EUCALYPTUS ,DAGGER nematodes ,RIBOSOMAL RNA ,PHYLOGENY ,VULVA ,ANATOMY - Abstract
A new dagger nematode, Xiphinema poasense n. sp., is described and illustrated from three populations extracted from soil associated with a combined plantation of Eucalyptus sp., Cupressus sp. and Pennisetum sp. and wild plants from a tropical premontane forest in Costa Rica. The new dagger nematode is characterised by a moderate body size 2612 (2416-3042) µm long, a rounded lip region 15.0 (13.5-16.5) µm broad, separated from the body contour by a shallow depression, amphidial fovea large, stirrupshaped, a very long odontostyle (175 (164-188) µm), stylet guiding ring located 167 (136-181) µm from anterior end, vulva situated anterior to mid-body (36-40%), anterior genital branch complete but strongly reduced, without uterine differentiation, female tail short, hemispherical to convex-conoid with a c' ratio = 0.7 (0.6-0.8) and bearing two pairs of caudal pores, and male absent. Integrative diagnosis was completed with molecular data using D2-D3 expansion segments of 28S rRNA, ITS1 region, partial 18S-rRNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). The phylogenetic relationships based on D2-D3 segments of this species with other Xiphinema spp. of the X. non-americanum group indicated that X. poasense n. sp. clustered with other species with a reduced anterior genital branch from the morphospecies Group 2, viz., X. costaricense and X. krugi. However, the phylogeny of coxI and partial 18S rRNA gene revealed that the new species did not cluster with Xiphinema species having the anterior genital branch absent or reduced (i.e., morphospecies Groups 1 and 2, respectively). [ABSTRACT FROM AUTHOR]
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- 2018
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23. Molecular phylogenetic analysis and comparative morphology resolve two new species of olive-tree soil related dagger nematodes of the genus Xiphinema (Dorylaimida : Longidoridae) from Spain.
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Archidona-Yuste, Antonio, Navas-Cortés, Juan A., Cantalapiedra-Navarrete, Carolina, Palomares-Rius, Juan E., and Castillo, Pablo
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MOLECULAR phylogeny ,DAGGER nematodes ,NEMATODE-plant relationships ,RIBOSOMAL RNA ,OLIVE ,COMPARATIVE biology - Abstract
The genus Xiphinema constitutes a large group of ~275 species of polyphagous, plant-ectoparasitic nematodes that are distributed almost worldwide. Some species affect agricultural crops by feeding directly on root cells as well as by transmitting nepoviruses. Despite their agricultural importance, species discrimination in Xiphinema is difficult, leading to potential misidentification. Integrative taxonomy, based on the combination of molecular analyses and morphology, constitutes a new insight into Xiphinema species identification. In this study we describe two new species of Xiphinema from the Iberian Peninsula (X. macrodora, sp. nov. and X. oleae, sp. nov.) associated with cultivated and wild olive trees. Both species have specific rRNA sequences. Morphologically, Xiphinema macrodora, sp. nov. is characterised by a very long body (7.2-8.7 mm), a very long odontostyle and odontophore (190-206 and 105-120 µm, respectively), and a well developed pseudo-Z-organ, comprising 8 to 12 sclerotised bodies. Xiphinema oleae, sp. nov. is characterised by an odontostyle and an odontophore 136-149 and 65-80 µm long, respectively, and a well developed Z-organ with refractive inclusions (3-5), variable in shape. Additionally, X. macrodora, sp. nov. has the longest body size, and the longest odontostyle and odontophore of any Xiphinema, whereas X. oleae, sp. nov. is the first species with a well developed Z-organ from the Iberian Peninsula. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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24. Cryptic diversity and species delimitation in the X iphinema americanum-group complex ( Nematoda: Longidoridae) as inferred from morphometrics and molecular markers.
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Archidona-Yuste, Antonio, Navas-Cortés, Juan A., Cantalapiedra-Navarrete, Carolina, Palomares-Rius, Juan E., and Castillo, Pablo
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SPECIES diversity ,CYTOCHROME oxidase ,RIBOSOMAL DNA ,METALLOENZYMES ,OXIDOREDUCTASES - Abstract
The X iphinema americanum-group constitutes a complex of about 55 species of polyphagous plant-ectoparasitic nematodes with a worldwide distribution. This group of plant-parasitic nematodes is one of the most difficult dagger nematode species complexes for diagnosis because the morphology is very conservative and morphometric characters often overlap. We conducted nematode surveys in cultivated and wild olives in southern Spain from 2012 to 2014, from which we identified 16 nematode populations of the X . americanum-group, five of which were tentatively identified as belonging to three new species and are described herein as X iphinema plesiopachtaicum sp. nov., X iphinema vallense sp. nov., and X iphinema astaregiense sp. nov., and 11 populations belonging to nine known species: X iphinema brevisicum, X iphinema duriense, X iphinema incertum, X iphinema luci, X iphinema madeirense, X iphinema opisthohysterum, X iphinema pachtaicum, X iphinema parapachydermum, and X iphinema rivesi. A phenetic study based on multivariate factor analyses was developed to compare some of these related species by using morphometric features. In the factor analysis the first four factors accounted for 73.1% of the total variance of the selected characters, identifying body length, body length/maximum body width (a), body length/pharyngeal length (b), body length/tail length (c), and tail length/body width at anus (c′) ratios, distance from anterior end to vulva as percentage of body length ( V), stylet length, oral aperture-guiding ring distance, and lip region width as key morphometric characters to differentiate a restricted set of species within the X. pachtaicum-subgroup that includes X. plesiopachtaicum sp. nov. and X. vallense sp. nov. Multivariate analysis of variance using these specific characters allowed to differentiate species in the X. pachtaicum complex or groups of them using morphometric characters (body length, a, b, c, c′, V, stylet length, lip region width, oral aperture-guiding ring distance, female tail length, and hyaline region length). Phylogenetic analyses based on nuclear ribosomal DNA genes [ D2- D3 expansion segments of large ribosomal subunit 28S, and internal transcribed spacer 1 ( ITS1)] and the protein-coding mitochondrial gene, cytochrome c oxidase subunit 1 ( coxI) were congruent, showing two main clades separating most of the species of X. americanum-subgroup ' sensu stricto' from the X. pachtaicum-subgroup. Agreement between phylogenetic trees and some morphological characters ( viz. total stylet length, vulva position, and a ratio) were tested by reconstruction of their histories on rRNA-based trees using parsimony and Bayesian approaches. Thus, integrative taxonomy, based on a combination of multivariate morphological and molecular analyses constitutes a new insight into the identification of X. americanum-group species. © 2015 The Linnean Society of London [ABSTRACT FROM AUTHOR]
- Published
- 2016
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25. Molecular variability and phylogenetic relationships among different species and populations of Pratylenchus (Nematoda: Pratylenchidae) as inferred from the analysis of the ITS rDNA.
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Luca, Francesca, Reyes, Aurelio, Troccoli, Alberto, and Castillo, Pablo
- Abstract
Sequence comparisons and molecular phylogenetic analyses were used to describe the nucleotide variability of the ITS containing regions of eighteen Pratylenchus species and several populations. Comparative analysis of nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among Pratylenchus species used in the present study demonstrates that ITS sequences can widely vary in primary sequence and length. Alignment of eighty-seven Pratylenchus sequences and one outgroup taxon reveals the presence of ambiguous regions that have the greatest effect on phylogeny reconstruction. Phylogenetic analyses using Bayesian Inference, Neighbour Joining-LogDet, Maximum Likelihood and Maximum Parsimony, distinguished twelve highly or moderately supported major clades within Pratylenchus. Our results support the taxonomic usefulness of the ITS region to identify root-lesion nematode species of the genus Pratylenchus but the high nucleotide variability, sometimes, can preclude its use to resolve relationships among all members of the genus. In addition, the phylogenetic groupings are not congruent with those defined by characters derived by lip patterns and numbers of lip annuli. [ABSTRACT FROM AUTHOR]
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- 2011
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26. Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain.
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CANTALAPIEDRA-NAVARRETE, Carolina, GUTIÉRREZ-GUTIÉRREZ, Carlos, LANDA, Blanca B., PALOMARES-RIUS, Juan E., and CASTILLO, Pablo
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DAGGER nematodes ,NEMATODES ,LONGIDORIDAE ,RECOMBINANT DNA - Abstract
During a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz., the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum, X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank. [ABSTRACT FROM AUTHOR]
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- 2011
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27. Molecular variability and phylogeny of Schistonchus caprifici (Gasperrini, 1864) Cobb, 1927 (Nematoda: Aphelenchoididae) from Italy and Spain.
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DE LUCA, Francesca, CASTILLO, Pablo, TROCCOLI, Alberto, VOVLAS, Nicola, LANDA, Blanca B., and PALOMARES-RIUS, Juan E.
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MOLECULAR phylogeny , *BAYESIAN analysis , *GENETIC polymorphisms , *CYTOCHROME oxidase , *PLANT genetics - Abstract
Molecular characterisation of four Schistonchus caprifici populations (two from Spain and two from Italy), using the partial 18S, the D2-D3 expansion segments of 28S of ribosomal DNA (rDNA) and the partial mitochondrial gene for cytochrome c oxidase I (mtCOI), is provided. Amplicons from partial mtCOI were analysed using 'Single Strand Conformation Polymorphism' (SSCP) analysis in order to rapidly screen for genetic (haplotypic) variability. SSCP analysis of mtCOI revealed a close relationship between the Spanish and Italian populations with low intra-population variability and only two haplotypes were detected. Mitochondrial COI and ribosomal genes were analysed using Maximum Likelihood and Bayesian inference to reconstruct phylogenetic relationships within S. caprifici and other members of the family Aphelenchoididae. The phylogenetic analysis based on mtCOI showed no geographic variability among Italian, Spanish and Turkish populations. The results of phylogenetic analyses based on the D2-D3 expansion segments of 28S rDNA region and the partial 18S rDNA genes revealed a closer phylogenetic relationship between S. aureus, S. laevigatus, S. virens and S. centerae, whilst S. caprifici and S. guangzhouensis clustered separately. The phylogeny of the genus Schistonchus was well related to some morphological characters, such as position of excretory pore, presence/absence of labial disc and number and position of caudal papillae. The monophyly of the genus Schistonchus was rejected by the Shimodaira-Hasegawa test based on tree topologies. [ABSTRACT FROM AUTHOR]
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- 2010
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28. Comparative morphometrics and ribosomal DNA sequence analysis of Longidorus orientalis Loof, 1983 (Nematoda: Longidoridae) from Spain and Iran.
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PALOMARES-RIUS, Juan E., LANDA, Blanca B., MAAFI, Zahra TANHA, HUNT, David J., and CASTILLO, Pablo
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BAYESIAN analysis ,RHIZOSPHERE ,NEEDLES (Botany) ,NEMATODES ,PHYLOGENY ,PLANT-soil relationships - Abstract
During recent nematode surveys in a muddy soil around undetermined graminaceous plants in El Rocío, Huelva Province, in southern Spain, and from the rhizosphere of date palm associated with graminaceous vegetation from Abadan, in Khuzestan Province, south-west Iran, populations of Longidorus orientalis were identified. Morphological and morphometrical studies on these populations fit the original description and represent the first report from Spain and Europe. Molecular characterisation of L. orientalis from Spain and Iran, using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS-rRNA, is provided. Sequences of the D2-D3 expansion regions and partial 18S genes were analysed using maximum likelihood and Bayesian inference to reconstruct phylogenetic relationships within L. orientalis and other Longidorus species. The results revealed a closer phylogenetic relationship with L. goodeyi for the D2-D3 expansion region and with L. vineacola for the partial 18S region. [ABSTRACT FROM AUTHOR]
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- 2010
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29. First Report of the Spiral Nematode Rotylenchus incultus (Nematoda: Hoplolaimidae) from Cultivated Olive in Tunisia, with Additional Molecular Data on Rotylenchus eximius.
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GUESMI-MZOUGHI, ILHEM, ARCHIDONA-YUSTE, ANTONIO, CANTALAPIEDRA-NAVARRETE, CAROLINA, REGAIEG, HAJER, HORRIGUE-RAOUANI, NAJET, PALOMARES-RIUS, JUAN E., and CASTILLO, PABLO
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NEMATODES ,ROTYLENCHUS ,OLIVE ,PLANT nematodes ,RHIZOSPHERE - Abstract
Spiral nematode species of the genus Rotylenchus have been reported on olive (Olea europaea L.) in several Mediterranean countries (Castillo et al., 2010; Ali et al., 2014). Nematological surveys for plant-parasitic nematodes on olive trees were carried out in Tunisia between 2013 and 2014, and two nematode species of Rotylenchus were collected from the rhizosphere of olive cv. Chemlali in several localities of Tunisia (Tables 1,2). Twenty-two soil samples of 3 to 4 kg were collected with a shovel from the upper 50 cm of soil from arbitrarily chosen olive trees. Nematodes were extracted from 500 cm³ of soil by centrifugal flotation method (Coolen, 1979). Specimens were heat killed by adding hot 4% formaldehyde solution and processed to pure glycerin using the De Grisse's (1969) method. Measurements were done using a drawing tube attached to a Zeiss III compound-microscope. Nematode DNA was extracted from single individuals and PCR assays were conducted as described by Castillo et al. (2003). Moderate-to-low soil populations of these spiral nematodes were detected (5.5-11.5, 1.5-5.0 individuals/500 cm³ of soil, respectively). This prompted us to undertake a detailed morphological and molecular comparative study with previous reported data. Morphological and molecular analyses of females identified these species as Rotylenchus eximius Siddiqi, 1964, and Rotylenchus incultus Sher, 1965. The morphology of R. eximius females (five specimens studied) was characterized by having a hemispherical lip region clearly off set, with four to five annuli, body without longitudinal striations, lateral fields areolated in the pharyngeal region only, stylet 32 to 36 mm long, and broadly rounded tail. The morphology of R. incultus females (51 females and 16 males; Table 2) was characterized by a hemispherical lip region with the basal annulus subdivided by irregular longitudinal striations, with three, rarely four annuli; stylet 21.5 to 27.5 mm long, female tail hemispherical with terminus regularly annulated; phasmids anterior to anus level (3-6 annuli above). The morphology of the isolated nematodes agreed with previous descriptions of R. eximius (Siddiqi, 1964; Castillo and Vovlas, 2005) and R. incultus (Sher, 1965; Castillo and Vovlas, 2005; Vovlas et al., 2008), respectively. A single individual was used for DNA extraction. Primers and PCR conditions used in this research were specified in Cantalapiedra-Navarrete et al. (2013), and a single amplicon of 800, 1,100, and 450 bp was obtained and sequenced for D2 to D3, ITS1, and cytochrome c oxidase subunit 1 (coxI), respectively. Sequence alignments for D2 to D3 (KX669231-KX669233), ITS1 (KX669238-KX669240), and cox I (KX669244-KX669245) from R. eximius, showed 99% to 97%, 98% to 94%, 93% similarity to other sequences of R. eximius deposited in GenBank (EU280794-DQ328741, EU373663-EU373664, JX015401-JX015402, respectively). Similarly, D2 to D3 (KX669234-KX669237), ITS1 (KX669241-KX669243), and coxI (KX669246-KX669249) sequence alignments from R. incultus, showed 99%, 99% to 95%, 99% to 90% similarity, respectively, to other sequences of R. incultus deposited in GenBank (EU280797, EU373672-EU373673, JX015403, respectively). The best fitted model of DNA evolution was obtained using µ Model Test v. 2.1.7 (Darriba et al. 2012) with the Akaike information criterion. BI analyses were performed under the general time reversible (GTR) with invariable sites and a gamma-shaped distribution of substitution rates (GTR + I + G) model for ITS1 and coxI. Phylogenetic analyses of ITS1 and coxI using Bayesian inference (BI) placed R. eximius and R. incultus from Tunisia in subclades that included all R. eximius and R. incultus sequences deposited in GenBank (Fig. 1), which agrees with previous results (Cantalapiedra-Navarrete et al., 2013). Morphology, morphometry, and molecular and phylogenetic data obtained from these samples were consistent with R. eximius and R. incultus identification. To our knowledge, this is the first report of R. incultus in Tunisia. Consequently, all these data suggest that spiral nematode species of the genus Rotylenchus are predominant in olive as previously reported in other Mediterranean areas (Ali et al., 2014). [ABSTRACT FROM AUTHOR]
- Published
- 2016
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30. Description and molecular characterisation of Paralongidorus litoralis sp. n. and P. paramaximus Heyns, 1965 (Nematoda: Longidoridae) from Spain.
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Palomares-Rius, Juan E., Subbotin, Sergei A., Landa, Blanca B., Vovlas, Nicola, and Castillo, Pablo
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NEMATODE anatomy ,SPECIES ,SAND dunes - Abstract
Paralongidorus litoralis sp. n., a new bisexual species of the genus, is described and illustrated by light microscopy, scanning electron microscopy and molecular studies from specimens collected in a coastal sand dune soil around roots of lentisc (Pistacia lentiscus L.) from Zahara de los Atunes (Cadiz), southern Spain. Paralongidorus litoralis sp. n. is characterised by the large body size (7.5-10.0 mm), a rounded lip region, clearly offset from the body by a collar-like constriction, and bearing a very large stirrup-shaped, amphidial fovea, with conspicuous slit-like aperture, a very long and flexible odontostyle ca 190 μm long, guiding ring located at 35 μm from anterior end, and males with spicules ca 70 μm long. In addition, identification data of a Spanish population of P. paramaximus Heyns, 1965 recovered from sandy soil of a commercial citrus orchard at Alcala de Guadaira (Seville), southern Spain, agree very well with the original description of the species from South Africa. The 18S rRNA and D2 and D3 expansion regions of 28S rRNA gene sequences were obtained for P. litoralis sp. n. and P. paramaximus. Phylogenetic analyses of P. litoralis sp. n. and P. paramaximus rRNA gene sequences and of Longidoridae sequences published in GenBank were done using maximum likelihood and Bayesian inference. In trees generated from the 18S data set Paralongidorus clustered as an external clade from Longidorus, and in trees generated from D2-D3 of 28S dataset Paralongidorus was monophyletic and nested within Longidorus. Maximum likelihood test supported the hypothesis of validity of the Paralongidorus genus. [ABSTRACT FROM AUTHOR]
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- 2008
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31. Pratylenchus vovlasi sp. Nov. (Nematoda: Pratylenchidae) on Raspberries in North Italy with a Morphometrical and Molecular Characterization †.
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Troccoli, Alberto, Fanelli, Elena, Castillo, Pablo, Liébanas, Gracia, Cotroneo, Alba, and De Luca, Francesca
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PRATYLENCHUS ,PLANT nematodes ,ROOT-knot nematodes ,BIOLOGICAL classification ,NEMATODES ,CYST nematodes ,RASPBERRIES ,HEAT shock proteins - Abstract
Root-lesion nematode species rank third only to root-knot and cyst nematodes as having the greatest economic impact on crops worldwide. A survey of plant-parasitic nematodes associated with decaying raspberries (Rubus sp.) in northern Italy revealed that root-lesion nematodes were the most frequently occurring species among other phytonematodes. Several Pratylenchus species have been associated with Rubus sp. in Canada (Quebec, British Columbia) and USA (North Carolina, Maryland, New Jersey) including P. penetrans and P. crenatus. In the roots and rhizosphere of symptomatic raspberries, nematodes of two Pratylenchus spp. were detected. Detailed morphometrics of the two root-lesion nematode isolates were consistent with Pratylenchus crenatus and with an undescribed Pratylenchus species. The extracted nematodes were observed and measured as live and fixed materials and subsequently identified by integrative taxonomy (morphometrically and molecularly). The latter species is described herein as Pratylenchus vovlasi sp. nov., resulting morphometrically closest to P. mediterraneus and phylogenetically to P. pratensis. The molecular identification of Pratylenchus vovlasi sp. nov. was carried out by sequencing the ITS region, D2-D3 expansion domains of the 28S rRNA gene and a partial region of the nuclear hsp90 gene. ITS-RFLP and sequence analyses revealed that Pratylenchus vovlasi sp. nov. had species-specific restriction profiles with no corresponding sequences present in the database. The phylogenetic relationships with ITS and D2-D3 sequences placed the Pratylenchus vovlasi sp. nov. in a clade with P. pratensis and P. pseudopratensis. This research confirms the occurrence of cryptic biodiversity within the genus Pratylenchus as well as the need for an integrative approach to the identification of Pratylenchus species. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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32. Global Distribution of the Reniform Nematode Genus Rotylenchulus with the Synonymy of Rotylenchulus macrosoma with Rotylenchulus borealis.
- Author
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Palomares-Rius, Juan E., Clavero-Camacho, Ilenia, Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, León-Ropero, Guillermo, Braun Miyara, Sigal, Karssen, Gerrit, and Castillo, Pablo
- Subjects
RIBOSOMAL DNA ,GENES ,NUCLEAR DNA ,MITOCHONDRIAL DNA ,TROPICAL climate ,CYTOCHROME oxidase - Abstract
Reniform nematodes of the genus Rotylenchulus are semi-endoparasites of numerous herbaceous and woody plant roots that occur largely in regions with temperate, subtropical, and tropical climates. In this study, we compared 12 populations of Rotylenchulusborealis and 16 populations of Rotylenchulusmacrosoma, including paratypes deposited in nematode collections, confirming that morphological characters between both nematode species do not support their separation. In addition, analysis of molecular markers using nuclear ribosomal DNA (28S, ITS1) and mitochondrial DNA (coxI) genes, as well as phylogenetic approaches, confirmed the synonymy of R. macrosoma with R. borealis. This study also demonstrated that R. borealis (= macrosoma) from Israel has two distinct rRNA gene types in the genome, specifically the two types of D2-D3 (A and B). We provide a global geographical distribution of the genus Rotylenchulus. The two major pathogenic species (Rotylenchulusreniformis and Rotylenchulusparvus) showed their close relationship with warmer areas with high annual mean temperature, maximum temperature of the warmest month, and minimum temperature of the coldest month. The present study confirms the extraordinary morphological and molecular diversity of R. borealis in Europe, Africa, and the Middle East and comprises a paradigmatic example of remarkable flexibility of ecological requirements within reniform nematodes. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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33. Morphostatic Speciation within the Dagger Nematode Xiphinema hispanum- Complex Species (Nematoda: Longidoridae).
- Author
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Archidona-Yuste, Antonio, Cai, Ruihang, Cantalapiedra-Navarrete, Carolina, Carreira, José A., Rey, Ana, Viñegla, Benjamín, Liébanas, Gracia, Palomares-Rius, Juan E., and Castillo, Pablo
- Subjects
MOLECULAR phylogeny ,NEMATODES ,SPECIES ,BIOLOGICAL classification ,CULTIVATED plants - Abstract
Dagger nematodes of the genus Xiphinema include a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We deciphered the cryptic diversity of the Xiphinema hispanum-species complex applying integrative taxonomical approaches that allowed us to verify a paradigmatic example of the morphostatic speciation and the description of a new species, Xiphinema malaka sp. nov. Detailed morphological, morphometrical, multivariate and genetic studies were carried out, and mitochondrial and nuclear haploweb analyses were used for species delimitation of this group. The new species belongs to morphospecies Group 5 from the Xiphinema nonamericanum-group species. D2-D3, ITS1, partial 18S, and partial coxI regions were used for inferring the phylogenetic relationships of X. malaka sp. nov. with other species within the genus Xiphinema. Molecular analyses showed a clear species differentiation not paralleled in morphology and morphometry, reflecting a clear morphostatic speciation. These results support the hypothesis that the biodiversity of dagger nematodes in southern Europe is greater than previously assumed. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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34. Molecular phylogenetic analysis and comparative morphology reveals the diversity and distribution of needle nematodes of the genus Longidorus (Dorylaimida: Longidoridae) from Spain.
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Archidona-Yuste, Antonio, Cantalapiedra-Navarrete, Carolina, Castillo, Pablo, and Palomares-Rius, Juan E.
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- *
MORPHOLOGY , *NEMATODES , *ECTOPARASITES , *PLANT viruses , *COMPARATIVE studies , *CULTIVATED plants , *WILD plants - Abstract
The genus Longidorus constitutes a large group of approximately 170 species of plant-ectoparasitic nematodes that are polyphagous and distributed almost worldwide. Some of the species of this genus are vectors of plant viruses. Species discrimination in Longidorus is difficult because the morphology is very conservative, and morphometric characters often overlap, leading to potential misidentification. Integrative taxonomy, based on the combination of molecular analyses with morphology, is a useful and necessary approach in Longidorus species identification. In Spain from 2014 to 2017, we conducted nematode surveys among cultivated and wild plants, from which we identified 13 populations of Longidorus, two of which appeared to represent new species and are described herein as L. iliturgiensis sp. nov. and L. pacensis sp. nov., and 11 populations belonging to eight known species: L. africanus, L. baeticus, L. carpetanensis, L. fasciatus, L. nevesi, L. cf. olegi, L. pini, and L. vallensis. Three species are new geographical records for Spain (L. nevesi, L. cf. olegi, and L. africanus). We report molecular data for L. nevesi, L. cf. olegi, L. carpetanensis and L. pini for the first time. Additionally, we describe the males of L. pini and the juveniles of L. cf. olegi. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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35. A new dagger nematode, Xiphinema poasense n. sp. (Nematoda: Longidoridae), from Costa Rica
- Author
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Carolina Cantalapiedra-Navarrete, Juan E. Palomares-Rius, Pablo Castillo, Walter Peraza-Padilla, Ingrid Varela-Benavides, Antonio Archidona-Yuste, Ministerio de Ciencia, Tecnología y Telecomunicaciones (Costa Rica), Consejo Nacional para Investigaciones Científicas y Tecnológicas (Costa Rica), Tecnológico de Costa Rica, Castillo, Pablo, and Castillo, Pablo [ 0000-0003-0256-876X]
- Subjects
Morphology ,0301 basic medicine ,Bayesian inference ,ITS1 ,18S ,Zoology ,Pennisetum sp ,18S ribosomal RNA ,03 medical and health sciences ,CoxI ,Xiphinema ,28S ribosomal RNA ,rRNA ,Longidoridae ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Taxonomy ,Morphometrics ,Nematology ,Pre-montane forest ,biology ,Cupressus sp. description ,Molecular ,biology.organism_classification ,Longidorids ,New species ,D2-D3 segments ,030104 developmental biology ,Nematode ,Taxonomy (biology) ,Eucalyptus sp ,Plant-parasitic nematode ,Agronomy and Crop Science - Abstract
A new dagger nematode, Xiphinema poasense n. sp., is described and illustrated from three populations extracted from soil associated with a combined plantation of Eucalyptus sp., Cupressus sp. and Pennisetum sp. and wild plants from a tropical pre-montane forest in Costa Rica. The new dagger nematode is characterised by a moderate body size 2612 (2416-3042) μm long, a rounded lip region 15.0 (13.5-16.5) μm broad, separated from the body contour by a shallow depression, amphidial fovea large, stirrup-shaped, a very long odontostyle (175 (164-188) μm), stylet guiding ring located 167 (136-181) μm from anterior end, vulva situated anterior to mid-body (36-40%), anterior genital branch complete but strongly reduced, without uterine differentiation, female tail short, hemispherical to convex-conoid with a c′ ratio = 0.7 (0.6-0.8) and bearing two pairs of caudal pores, and male absent. Integrative diagnosis was completed with molecular data using D2-D3 expansion segments of 28S rRNA, ITS1 region, partial 18S-rRNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). The phylogenetic relationships based on D2-D3 segments of this species with other Xiphinema spp. of the X. non-americanum group indicated that X. poasense n. sp. clustered with other species with a reduced anterior genital branch from the morphospecies Group 2, viz., X. costaricense and X. krugi. However, the phylogeny of coxI and partial 18S rRNA gene revealed that the new species did not cluster with Xiphinema species having the anterior genital branch absent or reduced (i.e., morphospecies Groups 1 and 2, respectively)., The first author (I. Varela) is a DOCINADE programme student and grateful for the grant from the Ministerio de Ciencia, Tecnología y Telecomunicaciones of Costa Rica and from Consejo Nacional para Investigaciones Científicas y Tecnológicas for her research stay at the IAS-CSIC. Research was supported by a grant from Vicerrectoría de Investigación, Instituto Tecnológico de Costa Rica.
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- 2018
36. Molecular and morphological characterization of the spiral nematode Helicotylenchus oleae Inserra, Vovlas & Golden, 1979 (Nematoda: Hoplolaimidae) in the Mediterranean Basin
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Pablo Castillo, Antonio Archidona-Yuste, Juan E. Palomares-Rius, Nicola Vovlas, Carolina Cantalapiedra-Navarrete, Emmanuel A. Tzortzakakis, Junta de Andalucía, European Commission, Ministerio de Economía y Competitividad (España), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Castillo, Pablo, and Castillo, Pablo [ 0000-0003-0256-876X]
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0106 biological sciences ,0301 basic medicine ,Bayesian inference ,D2-D3 ,010607 zoology ,rDNA ,Plant Science ,Horticulture ,01 natural sciences ,Mediterranean Basin ,Intraspecific competition ,03 medical and health sciences ,CoxI ,Phylogenetics ,Botany ,Helicotylenchus ,Phylogeny ,Taxonomy ,biology ,Phylogenetic tree ,biology.organism_classification ,New record ,030104 developmental biology ,Nematode ,Hoplolaimidae ,Taxonomy (biology) ,Its ,Agronomy and Crop Science - Abstract
The spiral nematode Helicotylenchus oleae is an ectoparasite of olive roots and is distributed in some countries in the Mediterranean Basin. In this study, we provided morphological and molecular characterisation of topotypes from southern Italy, as well as of several other populations from Crete (Greece) and Spain. Correct identification of plant-parasitic nematode species is essential to establish appropriate control strategies and for preventing their spread to other areas. Helicotylenchus oleae is reported for the first time in Greece (Crete). Integrative morphometric and molecular data for H. oleae populations using D2-D3 expansion segments of 28S rDNA, ITS-rDNA, and the cytochrome c oxidase subunit 1 (coxI), were in agreement with the original descriptions of the species, except for some minor differences, which may be a result of intraspecific variability. The phylogenetic relationships of this species with other representatives of Helicotylenchus spp. using D2-D3 expansion segments and the ITS-rRNA region was studied showing a low intraspecific diversity for H. oleae species. For the first time, coxI molecular data is obtained for the genus Helicotylenchus., This research was supported by grant P12-AGR 1486 from ‘Consejería de Economía, Innvovación y Ciencia’ from Junta de Andalucía, and Union Europea, Fondo Europeo de Desarrollo regional, ‘Una manera de hacer Europa’, grant 201740E042, "Análisis de diversidad molecular, barcoding, y relaciones filogenéticas de nematodos fitoparásitos en cultivos mediterráneos" from Spanish National Research Council (CSIC), grant KBBE 219262 ArimNET-ERANET FP7 2012-2015 Project PESTOLIVE ‘Contribution of olive history for the management of soilborne parasites in the Mediterranean basin’ from Hellenic Agricultural Organization-DEMETER and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), and AGL-2012-37521 from ‘Ministerio de Economía y Competitividad’ of Spain.
- Published
- 2017
37. Description and molecular phylogeny of one new and one known needle nematode of the genus Paralongidorus (Nematoda: Longidoridae) from grapevine in Portugal using integrative approach
- Author
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Manuel Mota, Carlos Gutiérrez-Gutiérrez, Pablo Castillo, Margarida Teixeira Santos, Juan E. Palomares-Rius, Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Junta de Andalucía, Castillo, Pablo [ 0000-0003-0256-876X], and Castillo, Pablo
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0106 biological sciences ,biology ,Phylogenetic tree ,Bayesian inference ,010607 zoology ,rDNA ,Plant Science ,Anatomy ,Horticulture ,Paralongidorus ,biology.organism_classification ,01 natural sciences ,Longidorids ,Nematode ,Sponge spicule ,Phylogenetics ,Molecular phylogenetics ,Taxonomy (biology) ,Longidoridae ,Agronomy and Crop Science ,Phylogeny ,010606 plant biology & botany ,Taxonomy - Abstract
A new and a known longidorid nematode, Paralongidorus lusitanicus n. sp. and Paralongidorus plesioepimikis, are described and illustrated from populations extracted from soil associated with grapevine (Vitis vinifera L.) from Escaroupim and Pó (central-Western Portugal), respectively. The new needle nematode P. lusitanicus n. sp. is characterised by a very large body size (8072–12,022 μm), an expanded and rounded lip region, ca 30 μm wide, with a clear constriction followed by a depression posterior to the amphidial aperture, amphidial fovea very large (11.0–19.0 μm), stirrup-shaped, with conspicuous slit-like aperture as shown in scanning electron microscopy studies, a very long and flexible odontostyle (180.0–223.0 μm), guiding ring located at 28.0–41.5 μm from anterior end, vulva anterior to the mid-body (34–41%), a dorsally convex-conoid tail with rounded terminus (29–42 μm long), bearing two or three pairs of caudal pores and males common (ratio 1:1.6 females) with spicules ca 80 μm long. Morphological and morphometric traits for P. plesioepimikis fit well with the original description, and is reported for the first time in Portugal. Integrative diagnosis of both species was completed with molecular data obtained using D2-D3 expansion segments of 28S rDNA, ITS1-rDNA and partial 18S–rDNA. The phylogenetic relationships of these species with other Paralongidorus spp. using these three molecular markers indicated that P. lusitanicus n. sp. clustered together with other Paralongidorus spp. forming a sister clade with P. plesioepimikis, both of them sharing a large body, long odontostyle, an anteriorly located vulva and an expanded and rounded lip region with a clear constriction followed by a depression posterior to the amphidial aperture., This research was financially supported by FCT - Foundation for Science and Technology postdoctoral fellowship SFRH/ BPD/95315/2013 and FEDER Funds through the Operational Programme for Competitiveness Factors - COMPETE and National Funds through FCT under the Strategic Projects PEst-C/AGR/UI0115/2011 and PEst-OE/ AGR/UI0115/2014 (Portugal). This research is partially supported by grant AGR-136 from ‘Consejería de Economía, Innvovación y Ciencia’ from Junta de Andalucía, and Union Europea, Fondo Europeo de Desarrollo regional, “Una manera de hacer Europa”.
- Published
- 2018
38. A new dagger nematode, Xiphinema tica n. sp. (Nematoda: Longidoridae), from Costa Rica with updating of the polytomous key of Loof and Luc (1990)
- Author
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Pablo Castillo, Tatiana Zamora-Araya, Carolina Cantalapiedra-Navarrete, Walter Peraza-Padilla, Antonio Archidona-Yuste, Juan E. Palomares-Rius, Universidad Nacional de Costa Rica, Fondo Institucional al Desarrollo Académico (Costa Rica), Ministerio de Economía y Competitividad (España), Castillo, Pablo [ 0000-0003-0256-876X], and Castillo, Pablo
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0106 biological sciences ,TAXONOMÍA ,Bayesian inference ,D2-D3 ,ITS1 ,010607 zoology ,18S ,rDNA ,Plant Science ,Horticulture ,Body size ,NEMÁTODA ,01 natural sciences ,Monophyly ,Phylogenetics ,CoxI ,Xiphinema ,Botany ,PLANTS ,Longidoridae ,Phylogeny ,Taxonomy ,biology ,Phylogenetic tree ,CROP ,CULTIVO ,biology.organism_classification ,Longidorids ,Nematode ,NEMATODA ,Taxonomy (biology) ,PLANTAS ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
A new dagger nematode, Xiphinema tica n. sp., is described and illustrated from several populations extracted from soil associated with several crops and wild plants in Costa Rica. The new dagger nematode is characterised by a moderate body size (3276–4240 μm), a rounded lip region, ca 13.5 μm wide, separated from body contour by a shallow depression, amphidial fovea large, stirrup-shaped, a moderately long odontostyle ca 135 μm long, stylet guiding ring located at ca 122 μm from anterior end, vulva almost equatorial (50–54%), well-developed Z-organ, with heavy muscularised wall containing in the most of specimens observed two moderately refractive inclusions variable in shape (from round to star-shaped), with uterine spines and crystalloid bodies; female tail short, dorsally convex-conoid, with rounded end and a small peg, with a c’ ratio ca 0.8, bearing two or three pairs of caudal pores and male absent. The unique and novel uterine differentiation based on the coexistence of a well-developed Z-organ mixed with uterine spines and crystalloid bodies in Xiphinema prompted us to update and include this combination of characters in the polytomous key of Loof and Luc (1990). Integrative diagnosis was completed with molecular data obtained, using D2-D3 expansion segments of 28S rDNA, ITS1-rDNA, partial 18S–rDNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). The phylogenetic relationships of this species with other Xiphinema spp. indicated that X. tica n. sp. was monophyletic to the other species from the morphospecies Group 4, Xiphinema oleae., Research was supported by grant of Universidad Nacional and FIDA (Fondo Institucional al Desarrollo Académico) from Costa Rica. The fourth author is a recipient of a “Juan de La Cierva” contract from Ministerio de Economía y Competitividad of Spain.
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- 2018
39. First Report of the Spiral Nematode Rotylenchus incultus (Nematoda: Hoplolaimidae) from Cultivated Olive in Tunisia, with Additional Molecular Data on Rotylenchus eximius
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Ilhem Guesmi-Mzoughi, Carolina Cantalapiedra-Navarrete, Pablo Castillo, Hajer Regaieg, Najet Horrigue-Raouani, Juan E. Palomares-Rius, Antonio Archidona-Yuste, Castillo, Pablo [ 0000-0003-0256-876X], and Castillo, Pablo
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0301 basic medicine ,Rhizosphere ,Morphology (linguistics) ,Phylogenetic tree ,Bayesian inference ,Biology ,biology.organism_classification ,Spiral nematodes ,Olive trees ,03 medical and health sciences ,Research Note ,Detection ,030104 developmental biology ,Nematode ,lcsh:Biology (General) ,Genus ,Phylogenetics ,Olea ,Botany ,lcsh:QH301-705.5 ,Phylogeny ,New geographic record - Abstract
Spiral nematode species of the genus Rotylenchus have been reported on olive (Olea europaea L.) in several Mediterranean countries (Castillo et al., 2010; Ali et al., 2014). Nematological surveys for plant-parasitic nematodes on olive trees were carried out in Tunisia between 2013 and 2014, and two nematode species of Rotylenchus were collected from the rhizosphere of olive cv. Chemlali in several localities of Tunisia (Tables 1,,2Table2). Twenty-two soil samples of 3 to 4 kg were collected with a shovel from the upper 50 cm of soil from arbitrarily chosen olive trees. Nematodes were extracted from 500 cm3 of soil by centrifugal flotation method (Coolen, 1979). Specimens were heat killed by adding hot 4% formaldehyde solution and processed to pure glycerin using the De Grisse’s (1969) method. Measurements were done using a drawing tube attached to a Zeiss III compound microscope. Nematode DNA was extracted from single individuals and PCR assays were conducted as described by Castillo et al. (2003). Moderate-to-low soil populations of these spiral nematodes were detected (5.5–11.5, 1.5–5.0 individuals/500 cm3 of soil, respectively)., This prompted us to undertake a detailed morphological and molecular comparative study with previous reported data. Morphological and molecular analyses of females identified these species as Rotylenchus eximius Siddiqi, 1964, and Rotylenchus incultus Sher, 1965. The morphology of R. eximius females (five specimens studied) was characterized by having a hemispherical lip region clearly off set, with four to five annuli, body without longitudinal striations, lateral fields areolated in the pharyngeal region only, stylet 32 to 36 μm long, and broadly rounded tail. The morphology of R. incultus females (51 females and 16 males; Table 2) was characterized by a hemispherical lip region with the basal annulus subdivided by irregular longitudinal striations, with three, rarely four annuli; stylet 21.5 to 27.5 μm long, female tail hemispherical with terminus regularly annulated; phasmids anterior to anus level (3–6 annuli above). The morphology of the isolated nematodes agreed with previous descriptions of R. eximius (Siddiqi, 1964; Castillo and Vovlas, 2005) and R. incultus (Sher, 1965; Castillo and Vovlas, 2005; Vovlas et al., 2008), respectively. A single individual was used for DNA extraction. Primers and PCR conditions used in this research were specified in Cantalapiedra-Navarrete et al. (2013), and a single amplicon of 800, 1,100, and 450 bp was obtained and sequenced for D2 to D3, ITS1, and cytochrome c oxidase subunit 1 (coxI), respectively. Sequence alignments for D2 to D3 (KX669231-KX669233), ITS1 (KX669238-KX669240), and coxI (KX669244-KX669245) from R. eximius, showed 99% to 97%, 98% to 94%, 93% similarity to other sequences of R. eximius deposited in GenBank (EU280794-DQ328741, EU373663-EU373664, JX015401-JX015402, respectively). Similarly, D2 to D3 (KX669234-KX669237), ITS1 (KX669241-KX669243), and coxI (KX669246-KX669249) sequence alignments from R. incultus, showed 99%, 99% to 95%, 99% to 90% similarity, respectively, to other sequences of R. incultus deposited in GenBank (EU280797, EU373672-EU373673, JX015403, respectively). The best fitted model of DNA evolution was obtained using jModelTest v. 2.1.7 (Darriba et al. 2012) with the Akaike information criterion. BI analyses were performed under the general time reversible (GTR) with invariable sites and a gamma-shaped distribution of substitution rates (GTR + I + G) model for ITS1 and coxI. Phylogenetic analyses of ITS1 and coxI using Bayesian inference (BI) placed R. eximius and R. incultus from Tunisia in subclades that included all R. eximius and R. incultus sequences deposited in GenBank (Fig. 1), which agrees with previous results (Cantalapiedra-Navarrete et al., 2013). Morphology, morphometry, and molecular and phylogenetic data obtained from these samples were consistent with R. eximius and R. incultus identification. To our knowledge, this is the first report of R. incultus in Tunisia. Consequently, all these data suggest that spiral nematode species of the genus Rotylenchus are predominant in olive as previously reported in other Mediterranean areas (Ali et al., 2014).
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- 2016
40. 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
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Subbotin, Sergei A., Sturhan, Dieter, Vovlas, Nicola, Castillo, Pablo, Tambe, James Tanyi, Moens, Maurice, and Baldwin, James G.
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NEMATODES , *BIOLOGICAL evolution , *NUCLEIC acid analysis , *NUCLEOTIDE sequence - Abstract
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. [Copyright &y& Elsevier]
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- 2007
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