research-article
overlapping ranges of measurements (Callejón et al., 2015, 2016; Vejl et al., 2017) and host preference may be more variable than previously thought (Doležalová et al., 2015). Approximately 24 species been reported from rodents, many of which exhibit comparable morphological patterns (Robles et al., 2014; Doležalová et al., 2015; Eberhardt et al., 2019).
Understanding the diversity and phylogeny of whipworms is important; false classification limits our acuity of biogeography and conceals the zoonotic
Malorri R. Hughes,
Deborah A. Duffield,
Dana K. Howe,
Dee R. Denver
Journal of Nematology , 1–6
research-article
classification from species level up to family level (Andrássy, 2007; Brzeski, 1998; Qing and Bert, 2019; Siddiqi, 2000).
With the improved availability of genetic sequencing, molecular sequences in species diagnosis and phylogeny analysis have consolidated them as one of the most powerful tools in current taxonomy. Among marker genes, the ribosomal RNA (rRNA) genes are being used as the standard barcode for almost all animals and successfully resolved several groups in Nematoda (Bert et al., 2008; Holterman
Mengxin Bai,
Xue Qing,
Kaikai Qiao,
Xulan Ning,
Shun Xiao,
Xi Cheng,
Guokun Liu
Journal of Nematology , 1–12
Article
Hemicycliophora. The 18S rDNA dataset was insufficient for distinguishing genus boundaries between Criconema, Ogma, and Crossonema. The relationships depicted by the 18S rDNA phylogeny suggest that key morphological characters used in the classification of Criconematidae are not homologous.
THOMAS POWERS,
TIMOTHY HARRIS,
REBECCA HIGGINS,
PETER MULLIN,
KIRSTEN POWERS
Journal of Nematology , ISSUE 3, 236–244
research-article
Hossein Mirbabaei Karani,
Ali Eskandari,
Reza Ghaderi,
Akbar Karegar
Journal of Nematology , 1–17
Research Article
Mehrdad Madani,
Mario Tenuta
Journal of Nematology , ISSUE 2, 163–182
research-article
and Renčo (2007; Slovakia), Carrión and Desgarennes (2012; Mexico), Gagarin (2018; Vietnam), and Shurkurovich and Akvarovna (2018; Uzbekistan).
Phylogeny and systematics of Eucephalobus
Diagnosis (emended)
Cephalobidae, Cephalobinae: they are small nematodes, 0.36 to 1.00 mm long, cuticle bearing transverse striation, lateral field with three longitudinal incisures, lip region continuous with the adjacent body and consisting of conoid lips, primary and secondary axils showing similar
Joaquín Abolafia,
Reyes Peña-Santiago
Journal of Nematology , 1–20
Article
as the closely related Ottolenchus were given based on a combination of morphology and recent molecular data, and their phylogeny were analyzed in a context of Tylenchidae. Furthermore, we test different fungi and moss as a food resource of Malenchus and their feeding behavior is also discussed.
XUE QING,
WIM BERT
Journal of Nematology , ISSUE 2, 189–206
Research Article
The 18S small subunit (SSU) ribosomal DNA sequence is one of the most useful molecular loci for identification and phylogeny reconstruction of agriculturally important nematodes. Various pairs of universal primers have been developed in the past to amplify short and long nematode sequences. However, certain nematode taxa were not readily amplified and/or sequenced with the existing primer tools. Frequently, the center region of a roughly 1,000 nucleotide segment would be lost. Therefore new
L. K. Carta,
S. Li
Journal of Nematology , ISSUE 4, 533–542
research-article
clustering (PP = 81%) with two isolates of an unknown species of Coslenchus (JQ005005 and JQ005006), but separated from the sequences of other Coslenchus species.
Figure 5:
Figure 5: The 50% majority rule consensus trees from Bayesian analysis generated from the D2–D3 expansion fragments of 28 S rRNA gene dataset under GTR+I+G model. Posterior probabilities for BI analysis more than 50% are given for appropriate clades. New sequences are indicated in bold.
Discussion
In our phylogeny tree, the
Manouchehr Hosseinvand,
Ali Eskandari,
Reza Ghaderi
journal of nematology , 1–10
research-article
allowance for gamma distribution of rate variation (GTR+Γ) in RAxML v8 (Stamatakis, 2014). The phylogeny of Helicotylenchus was inferred using MrBayes v3.2.6 (Ronquist et al., 2012) with the GTR + Γ model. Two independent Metropolis-coupled Markov chain Monte Carlo (MCMCMC) searches were performed for 2 million generations sampling every 2,000 steps. Convergence was assessed using Tracer v1.5 (burn-in = 20% of the samples), and by examining the average standard deviation of split frequencies among
Donald Riascos-Ortiz,
Ana Teresa Mosquera-Espinosa,
Francia Varón De Agudelo,
Claudio Marcelo Gonçalves de Oliveira,
Jaime Eduardo Muñoz-Florez
Journal of Nematology , 1–19
Research Article
rRNA gene, D2–D3 expansion domains of the 28S rDNA, the ITS region, and the partial mitochondrial COI were carried out. Sequences of the 18S rRNA gene, the D2–D3 domains, and the ITS were analyzed using several methods for inferring phylogeny to reconstruct the relationships among Sheraphelenchus and Bursaphelenchus species. The bacterial feeder Panagrellus sp. was characterized at the molecular level only. The D2–D3 expansion domains and ITS sequences of this Italian panagrolaimid were determined
ELENA FANELLI,
ALBERTO TROCCOLI,
NICOLA VOVLAS,
GIANLUCA SCARCIA,
ANNAMARIA MINCUZZI,
SIMONA M. SANZANI,
ANTONIO IPPOLITO,
FRANCESCA DE LUCA
Journal of Nematology , ISSUE 4, 418–426
Original Paper
all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. For these two kinds of rocks, Proteobacteria was the first dominant group, and Gammaproteobacteria occupied the greatest proportion which might be closely related to Pseudomonas in phylogeny to be the most dominant genera after isolation. Actinobacteria and Bacillus bacteria were also widespread in these two kinds of rock environments
Yuan Tang,
Jian-Zhong Cheng,
Bin Lian
Polish Journal of Microbiology , ISSUE 4, 413–423
Original Paper
MARISELA YADIRA SOTO-PADILLA,
PABLO GORTÁRES-MOROYOQUI,
LUIS ALBERTO CIRA-CHÁVEZ,
MARÍA ISABEL ESTRADA-ALVARADO
Polish Journal of Microbiology , ISSUE 3, 377–382
research-article
with the SSU rDNA of S. hyrcania (KT354242). The identity value with other sequences was all less than 91%.
A number of 38 ektaphelenchid+seinurid, a Noctuidonema sp., an Anomyctus sp., an Peraphelenchus sp., two aphelenchid and three rhabditid SSU sequences were selected for the SSU phylogeny. A number of 52 ektaphelenchid + seinurid, a Noctuidonema sp., two aphelenchid and three rhabditid LSU D2-D3 sequences were selected for the LSU phylogeny. The selection of the sequences for both analyses was
Jianfeng Gu,
Munawar Maria,
Lele Liu,
Majid Pedram
Journal of Nematology , 1–11
research-article
Hadi Karimipour Fard,
Hamid Zare
Journal of Nematology , 1–3
Research Article
Victor Phani,
Satyapal Bishnoi,
Amita Sharma,
Keith G. Davies,
Uma Rao
Journal of Nematology , ISSUE 3, 387–398
research-article
L. K. Carta,
S. Li
Journal of Nematology , 1–8
research-article
accession numbers given in LSU and ITS1 trees.
Phylogenetic analyses
The newly generated sequences were compared with the available sequences in the GenBank database using the basic local alignment search tool (BLAST) (https:// blast.ncbi.nlm.nih.gov/Blast.cgi). For LSU phylogeny, several available sequences of the genus were retrieved from the database (a large and a smaller pruned LSU datasets were prepared). The currently available ITS1 sequences of Longidorus spp. were retrieved for the ITS1
Mazdosht Giti,
Leila Kashi,
Majid Pedram
journal of nematology , 1–11
Article
LYNN K. CARTA,
SHIGUANG LI,
ANDREA M. SKANTAR,
GEORGE NEWCOMBE
Journal of Nematology , ISSUE 1, 28–33
Article
MAJID PEDRAM
Journal of Nematology , ISSUE 2, 223–230
Research Article
Ilia Mariana Escobar-Avila,
Edgar Óliver López-Villegas,
Sergei A. Subbotin,
Alejandro Tovar-Soto
Journal of Nematology , ISSUE 2, 229–242
Article
ILHEM GUESMI-MZOUGHI,
ANTONIO ARCHIDONA-YUSTE,
CAROLINA CANTALAPIEDRA-NAVARRETE,
HAJER REGAIEG,
NAJET HORRIGUE-RAOUANI,
JUAN E. PALOMARES-RIUS,
PABLO CASTILLO
Journal of Nematology , ISSUE 3, 136–138
Article
MEHRAB ESMAEILI,
RAMIN HEYDARI,
WEIMIN YE
Journal of Nematology , ISSUE 2, 109–115
Article
ALI YAGHOUBI,
EBRAHIM POURJAM,
SERGIO A LVAREZ-ORTEGA,
GRACIA LIE´BANAS,
MOHAMMAD REZA ATIGHI,
MAJID PEDRAM
Journal of Nematology , ISSUE 3, 214–221
Research Article
L. K. Carta,
W. K. Thomas,
V. B. Meyer-Rochow
Journal of Nematology , ISSUE 4, 479–486
research-article
Paurodontus by having the stylet with asymmetrical basal knobs (vs asymmetrical), and by the presence of a rudimentary PUS (vs prominent). It can also be distinguished from Paurodontoides by having a rudimentary PUS (vs prominent) and having a leptoderan (vs peloderan) bursa.
Molecular phylogeny
The amplification of the partial 28S D2/D3 rDNA gene sequence from Paurodontella composticola n. sp. specimens yielded a single fragment of approximately 800 bp based on gel size.
To determine the phylogenetic
Mehrab Esmaeili,
Ramin Heydari,
Ahmad Kheiri,
Weimin Ye
Journal of Nematology , 1–12
research-article
phylogenetic studies have focused specifically on Cephalenchus, investigating several aspects of its evolution including inter- and intraspecies and intragenomic variations, correlation of morphology and phylogeny and biogeography (Pereira and Baldwin, 2016; Pereira et al., 2017).
During our recent surveys in South Africa, a population of Cephalenchus with a remarkably short stylet, long pharyngeal overlap, and four lines in the lateral field was recovered from the rhizosphere of grasses near a maize field
Milad Rashidifard,
Gerhard Du Preez,
Joaquín Abolafia,
Majid Pedram
Journal of Nematology , 1–10
research-article
other Aphelenchus species is usually short, collapsed, or shrink, without sperm.
Molecular characterization and phylogeny
The sequences of nearly full-length 18S (1707 bp, GenBank accession numbers MT396110- MT396111), 28S D2-D3 region (772 bp, MT396108-MT396109) and ITS region of rDNA (661 bp, MT396103-MT396104) of A. yinyuensis n. sp. were obtained. Phylogenetic relationships among the isolates were determined separately for each dataset using Bayesian inference (BI), with Caenorhabditis
Gu Jianfeng,
Munawar Maria,
Yiwu Fang,
Liu Lele,
Xianfeng Chen,
Bo Cai
Journal of Nematology , 1–12
research-article
poinari (Aliramaji et al., 2014) revealed that a slightly projecting structure is present slightly anterior to the cloacal opening. This could be the single precloacal P1 papilla, or the paired papillae, similar to those in E. pini. The last pair is situated at 14.5 µm distance to the tail tip. The arrangement and number of papilla for this species are amended herein.
Molecular characterization and phylogenetic relationships
Partial SSU rDNA phylogeny
To determine the phylogenetic relationships of
Fariba Heydari,
Majid Pedram
Journal of Nematology , 1–12
Article
MEHRAB ESMAEILI,
RAMIN HEYDARI,
MOZHGAN ZIAIE,
JIANFENG GU
Journal of Nematology , ISSUE 1, 34–42
Article
YOUSEF PANAHANDEH,
EBRAHIM POURJAM,
MAJID PEDRAM
Journal of Nematology , ISSUE 4, 268–279
research-article
Ebrahim Shokoohi,
Joaquín Abolafia,
Phatu William Mashela,
Nafiseh Divsalar
Journal of Nematology , 1–26
research-article
Hossein Mirbabaei,
Ali Eskandari,
Reza Ghaderi,
Akbar Karegar
Journal of Nematology , 1–14
Article
BEHROUZ GOLHASAN,
RAMIN HEYDARI,
MEHRAB ESMAEILI,
ESMAEIL MIRAEIZ
Journal of Nematology , ISSUE 1, 67–76
Research Article
Munawar Maria,
Ruihang Cai,
Weimin Ye,
Thomas O. Powers,
Jingwu Zheng
Journal of Nematology , ISSUE 4, 611–622
research-article
Jianfeng Gu,
Munawar Maria,
Yiwu Fang,
Lele Liu,
Yong Bian,
Xianfeng Chen
Journal of Nematology , 1–1
research-article
using CLUSTAL W (Thompson et al., 1994). The length of each alignment was 946 and 1186 bp for ITS rDNA and 28S rDNA, respectively. Bayesian inference was used to reconstruct the phylogeny, with Bayesian trees generated using the Bayesian inference method as implemented in the program MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003). The GTR + I + G model was selected using jModeltest 2.1.10 (Guindon and Gascuel, 2003; Darriba et al., 2012). Analysis using the GTR + I + G model was initiated with a
Ebrahim Shokoohi,
Phatu W. Mashela
Journal of Nematology , 1–5
research-article
those in the basal clades. In the present study, we reported that a M. mali population was imported from Japan in Ningbo Port, China, with high intragenomic rRNA polymorphisms. We describe this population by detailed morphology and molecular phylogeny, and compare it with other populations in GenBank by mitochondrial COI haplotype network analysis.
Materials and methods
Isolation and morphological observation of nematodes
Roots and a little soil and rhizosphere medium associated with maple (Acer
Jianfeng Gu,
Yiwu Fang,
Lele Liu
Journal of Nematology , 1–11
Article
ZAFAR A. HANDOO,
LYNN K. CARTA,
ANDREA M. SKANTAR,
SERGEI A. SUBBOTIN,
STEPHEN W. FRAEDRICH
Journal of Nematology , ISSUE 1, 20–27
Research Article
Weimin Ye,
Shane Foye,
Ann E. MacGuidwin,
Shawn Steffan
Journal of Nematology , ISSUE 1, 9–26
Research Article
Farzad Aliramaji,
Ebrahim Pourjam,
Sergio Álvarez-Ortega,
Farahnaz Jahanshahi Afshar,
Majid Pedram
Journal of Nematology , ISSUE 3, 437–452
research-article
O. Gorgadze,
A. Troccoli,
E. Fanelli,
E. Tarasco,
F. De Luca
Journal of Nematology , 1–12
Article
HARUN CIMEN,
VLADIMI´R PU°zA,
JIRI NERMUT,
JUSTIN HATTING,
TSHIMA RAMAKUWELA,
SELCUK HAZIR
Journal of Nematology , ISSUE 3, 148–158
Article
MANUEL MUNDO-OCAMPO,
J. G. BALDWIN,
T. J. PEREIRA,
J. R. CAMACHO-BAEZ,
A. D. ARMENTA-BOJORQUEZ,
M. CAMACHO-HARO,
J. O. BECKER
Journal of Nematology , ISSUE 1, 103–113
research-article
. lapidosum seems to be related with X. lupini because of both species clustered together in all the analyses carried out in this study. The present study on the phylogeny based on D2 to D3 segments supported a very weak correlation in the phylogenetic relationships among the different morphospecies groups within Xiphinema, a finding already reported by several authors namely, Gutiérrez-Gutiérrez et al., 2013; De Luca et al., 2014; Tzortzakakis et al., 2014, 2015; Archidona-Yuste et al., 2016a, 2016b
Ruihang Cai,
Antonio Archidona-Yuste,
Carolina Cantalapiedra-Navarrete,
Juan E. Palomares-Rius,
Jingwu Zheng,
Pablo Castillo
Journal of Nematology , 1–21
research-article
-separated clades and grouped with species having shorter stylets and advuval flap, the species having longer stylets arranged at the basal position of the trees. To this point we suppose only fewer paratylenchid sequences were available for the phylogenetic studies, the inclusion of more sequences from other known species will be helpful to provide a better resolution of paratylenchid phylogeny.
Additional remarks
Ghaderi et al. (2014) presented a key for the species identification of pin nematodes
Munawar Maria,
Wentao Miao,
Weimin Ye,
Jingwu Zheng
journal of nematology , 1–13
research-article
Alemayehu W. Habteweld,
Faruk Akyazi,
Soumi Joseph,
William T. Crow,
Eyualem Abebe,
Tesfamariam Mekete
Journal of Nematology , 1–15
research-article
provided its diagnosis.
Sudhaus and Hooper (1994) provided new ideas about the taxonomy and the phylogeny of several rhabditid species: (i) accepted Oscheius as a subgenus of Rhabditis, (ii) regarded it as a monophyletic taxon based on three synapomorphies (long female rectum, terminal duct of the excretory system forwards coiled and with heavily sclerotized wall, and several features of spicule shape), (iii) considered Dolichorhabditis (Andrássy, 1983) as a junior synonym of Oscheius, and (iv
Joaquín Abolafia,
Reyes Peña-Santiago
journal of nematology , 1–21
Research Article
Farshad Gharibzadeh,
Ebrahim Pourjam,
Majid Pedram
Journal of Nematology , ISSUE 2, 207–218
Research Article
Yousef Panahandeh,
Joaquín Abolafia,
Ebrahim Pourjam,
Robin M. Giblin-Davis,
Farahnaz Jahanshahi Afshar,
Majid Pedram
Journal of Nematology , ISSUE 3, 343–354
Research Article
Maria Munawar,
Thomas O. Powers,
Zhongling Tian,
Timothy Harris,
Rebecca Higgins,
Jingwu Zheng
Journal of Nematology , ISSUE 2, 183–206
research-article
-morphological characterization presenting challenges in the taxonomy of criconematids. The phylogeny of the majority of criconematids taxa is not well resolved, and to this point, we only suggest that molecular identification can be an efficient way of identifying species; however, linking the correct molecular information to the detected species is an important aspect. The generic status of new species is assigned primarily on the basis of morphological characters of females and juveniles. This is the
Munawar Maria,
Wentao Miao,
Ruihang Cai,
Pablo Castillo,
Jingwu Zheng
Journal of Nematology , 1–14
research-article
, additional studies are required to shed light on the evolution, phylogeny, and ecological aspects of these nematodes.
Munawar Maria,
Wentao Miao,
Pablo Castillo,
Jingwu Zheng
Journal of Nematology , 1–13
Article
MAGDALENA OLSON,
TIMOTHY HARRIS,
REBECCA HIGGINS,
PETER MULLIN,
KIRSTEN POWERS,
SEAN OLSON,
THOMAS O. POWERS
Journal of Nematology , ISSUE 1, 42–66
Article
MEHRAB ESMAEILI,
RAMIN HEYDARI,
WEIMIN YE
Journal of Nematology , ISSUE 3, 268–275
research-article
fields (6 vs 10-12) and anteriorly located vulva (V = 89 (87.2-90.3) vs 92 (92-93)).
Molecular profiles and phylogenetic status
Nearly full length SSU rDNA phylogeny
To determine the phylogenetic relationships of D. brevis n. sp. with other species, a newly obtained 1674 nt nearly full length SSU rDNA sequence with accession number MT009494 was used. The BLAST search using this fragment revealed that it is unique, and its identity with other previously submitted sequences to the database is less
Fariba Heydari,
Joaquín Abolafia,
Majid Pedram
Journal of Nematology , 1–13
research-article
Journal of Nematology , 1–2
Research Article
LIRONG ZHAO,
WEIMIN YE,
MUNAWAR MARIA,
MAJID PEDRAM,
JIANFENG GU
Journal of Nematology , ISSUE 4, 404–417
research-article
morphology and morphometrics along with molecular characteristics and phylogeny of the D2-D3 expansion segment of 28S rDNA, ITS rDNA, and COI mtDNA sequences.
Materials and methods
Sampling and nematode extraction
The soil and root samples were collected around the rhizosphere of banana (Musa basjoo Siebold & Zucc. ex Iinuma) (GPS coordinates N: 51°2′6.8″, E: 3°43′22.7″) and Yam (Dioscorea tokoro) (GPS coordinates: N: 51°2′6.9″, E: 3°43′22.6″) at the Botanical garden of Ghent University. The nematodes
Huu Tien Nguyen,
Quang Phap Trinh,
Marjolein Couvreur,
Phougeishangbam Rolish Singh,
Wilfrida Decraemer,
Wim Bert
Journal of Nematology , 1–20
research-article
Phougeishangbam Rolish Singh,
Beatrice E. Kashando,
Marjolein Couvreur,
Gerrit Karssen,
Wim Bert
Journal of Nematology , 1–17
research-article
the most consistent tree representing the relationship of the P. curvicauda samples with other Pratylenchus species. These trees were constructed using the bootstrap method as a test of Phylogeny with 1,000 replicates, where necessary they are presented with the bootstrap values. Representative sequences of Meloidogyne spp. and Radopholus similis, derived from similar regions of the rDNA, were used as outgroups for the phylogenetic analyses.
Differences between and within sequences of either the
Farhana Begum,
John Fosu-Nyarko,
Shashi Sharma,
Bill Macleod,
Sarah Collins,
Michael G. K. Jones
Journal of Nematology , 1–15