Article | 03-December-2017
In the nematode family Criconematidae, a taxonomy primarily based on cuticle characters has created classifications that are notoriously volatile. Molecular characters may lead to their stabilization. A phylogenetic tree of Criconematoidea was constructed using 166 new near full-length 18S rDNA sequences and 58 sequences from GenBank. Bayesian and maximum likelihood (ML) analyses produced trees with similar topologies. Major features include a strongly supported clade that includes
THOMAS POWERS,
TIMOTHY HARRIS,
REBECCA HIGGINS,
PETER MULLIN,
KIRSTEN POWERS
Journal of Nematology, Volume 49 , ISSUE 3, 236–244
research-article | 06-June-2019
process as well as to delineate more phylogenetically distant species, which share the same morphology (cryptic species), the support of a molecular approach is needed.
To date, only about 20% of Helicotylenchus species has been molecularly characterized using mostly ribosomal DNA fragments (18S, ITS, 28S rDNA; GenBank resources). Mitochondrial cytochrome c oxidase subunit I (mtCOI) sequences were reported for one species, the recently described H. oleae (Palomares-Rius et al., 2018), and a cytochrome
K. Rybarczyk-Mydłowska,
E. Dmowska,
K. Kowalewska
Journal of Nematology, Volume 51 , 1–17
Research Article | 17-October-2018
duct, offset spermatheca filled with small spheroid sperm cells, 106 to 127 µm long elongate-conoid tail with filiform distal region and finely rounded tip. Molecular phylogenetic analyses were performed using a near-full length fragment of the 18S rDNA and the D2–D3 expansion segments of the 28S rDNA using Bayesian inference and maximum likelihood methods. In the inferred phylogenetic tree with 18S rDNA, the new species has a close affinity with several isolates of the type species, Labrys
Yousef Panahandeh,
Joaquín Abolafia,
Ebrahim Pourjam,
Robin M. Giblin-Davis,
Farahnaz Jahanshahi Afshar,
Majid Pedram
Journal of Nematology, Volume 50 , ISSUE 3, 343–354
research-article | 26-March-2021
at 16,000 rpm (Shokoohi et al., 2020). The supernatant was then extracted from each of the tubes and stored at –20°C. Following this step, the forward and reverse primers, SSU F04 (5’–GCTTGTCTCAAAGATTAAGCC–3’) and SSU R26 (5’–CATTCTTGGCAAATGCTTTCG–3’) (Blaxter et al., 1998) for 18 S rDNA and D2A (5’–ACAAGTACCGTGAGGGAAAGTTG–3’), D3B (5’–TCGGAAGGAACCAGCTACTA–3’) (De Ley et al., 1999) for 28 S rDNA, were used in the PCR reactions for partial amplification of the 18 S rDNA, and 28 S rDNA regions. PCR
Ebrahim Shokoohi
Journal of Nematology, Volume 53 , 1–9
Research Article | 03-September-2018
molecular analysis of many D. weischeri specimens from Canada is presented. Individuals from 41C. arvense or yellow pea grain samples with seeds of C. arvense from the Prairie Provinces were sequenced for the internal transcribed spacer (ITS rDNA), large subunit (LSU) D2D3 28S rDNA, partial segment of small subunit (SSU) 18S rDNA, and the heat shock protein Hsp90 gene. The analysis also included D. weischeri individuals from C. arvense from Russia and garlic with D. dipsaci from the Provinces of Ontario
Mehrdad Madani,
Mario Tenuta
Journal of Nematology, Volume 50 , ISSUE 2, 163–182
research-article | 03-June-2019
Eukaryotic nuclear ribosomal DNA (rDNA) is arranged in tandem repeat arrays in the genome. Each repeat unit consists of one copy of small subunit (SSU) 18S, internal transcribed spacers (ITS1 and ITS2), 5.8S, and large subunit (LSU) 28S rDNA, and is separated by an external transcribed spacer (EST) and an intergenic spacer (IGS) (Hillis and Dixon, 1991). The copy number of the repeats within most eukaryotic genomes is high, which provide large quantities of template DNA for PCR. In
L. K. Carta,
S. Li
Journal of Nematology, Volume 51 , 1–8
Article | 24-July-2017
SEM study of the genus. These results confirmed longitudinal amphidial aperture type on lateral sides of the lip region in genus Discotylenchus, as noted by Siddiqi while erecting the genus with D. discretus as the type species. Molecular phylogenetic analyses using partial small subunit (SSU) and large subunit (LSU) rDNA sequences revealed the affinity of the genus Discopersicus n. gen. with members of the subfamily Boleodorinae, as supported by morphological characters (mainly, the oblique
ALI YAGHOUBI,
EBRAHIM POURJAM,
SERGIO A LVAREZ-ORTEGA,
GRACIA LIE´BANAS,
MOHAMMAD REZA ATIGHI,
MAJID PEDRAM
Journal of Nematology, Volume 48 , ISSUE 3, 214–221
research-article | 30-November-2020
upon morphological and morphometric characteristics. Additionally, molecular data from LSU D2D3 and ITS rDNA markers were used to study the phylogenetic relationships with others Bitylenchus species.
Materials and methods
Nematode extraction and morphological observations
Several soil samples were collected from the rhizosphere of euphrates poplar (Populus euphratica Oliv.) trees in Khuzestan province, Iran. Centrifugal – flotation technique (Jenkins, 1964) or the tray method (Whitehead and
Abbas Abdolkhani,
Sedighe Azimi
Journal of Nematology, Volume 53 , 1–10
research-article | 14-December-2020
Jacob, 2012, and Oscheius amsactae Ali, Pervez, Andrabi, Sharma and Verma, 2011 and Metarhabditis longicaudata Tabassum, Salma and Nasir, 2019. Most of these studies, however, have characterized the species morphologically and morphometrically. Regarding molecular analysis, several Internal Transcribed Spacer (ITS) rDNA sequences, obtained from M. amsactae isolated in India, Philippines, and Pakistan have been deposited in the GenBank, but none of the nematode specimens used to obtain the sequences
Aashaq Hussain Bhat,
Shreyansh Srivastava,
Aasha Rana,
Ashok Kumar Chaubey,
Ricardo A. R. Machado,
Joaquín Abolafia
Journal of Nematology, Volume 52 , 1–23
Research Article | 03-September-2018
study. Molecular characterization based on 18SSU rDNA sequencing performed to confirm the taxonomic position of this species and to documents the morphological data. Sequence alignment detects a percent of identity up to 88.0% with other Heteroxynematidae species. Phylogenetic analysis showed that the present recorded is a putative sister taxon to A. tetraptera recorded in a previous study. The SSU rDNA sequence has been deposited in the GenBank under the accession no. MG019400.
Rewaida Abdel-Gaber,
Fathy Abdel-Ghaffar,
Saleh Al Quraishy,
Kareem Morsy,
Rehab Saleh,
Heinz Mehlhorn
Journal of Nematology, Volume 50 , ISSUE 2, 117–132
research-article | 30-November-2019
microscopy (SEM)
Specimens preserved in glycerine were selected for observation under SEM according to the methods of Abolafia (2015). They were hydrated in distilled water, dehydrated in a graded ethanol-acetone series, critical point dried, coated with gold, and observed with a Zeiss Merlin microscope (5 kV) (Zeiss, Oberkochen, Germany).
Phylogenetic analyses
For phylogenetic relationships, analyses were based on 18S and 28S rDNA gene sequences available in GenBank. The sequences were aligned using
Joaquín Abolafia,
Reyes Peña-Santiago
Journal of Nematology, Volume 52 , 1–20
research-article | 30-November-2018
Applied Biosystems Hitachi 3500 Genetic Analyzer. The sequences obtained were submitted to the GenBank database.
Phylogenetic analyses
For phylogenetic relationships, analyses were based on 18S and 28S rDNA. The newly obtained sequences were manually edited using BioEdit 7.2.6 (Hall, 1999) and aligned with another 18S or 28S rRNA gene sequences available in GenBank using Muscle alignment tool implemented in the MEGA7 (Kumar et al., 2016). The ambiguously aligned parts and divergent regions were
Joaquín Abolafia,
Reyes Peña-Santiago
journal of nematology, Volume 51 , 1–21
research-article | 30-November-2019
, measurements and pictures were taken using Carl Zeiss Axio Lab. A1 light microscope equipped with a Zeiss Axiocam ERc5s digital camera. For molecular characterization, the D2-D3 region of 28S rDNA and COI mtDNA gene were amplified using D2A/D3B (5′–ACAAGTACCGTGGGGAAAGTTG–3′/5′–TCGGAAGGAACCAGCTACTA–3′) (Subbotin et al., 2006) and JB3/JB4 (5′-TTTTTTGGGCATCCTGAGGTTTAT-3′/5′-TAAAGAAAGAACATAATGAAAATG-3′) (Nguyen et al., 2019b) primers. Forward and reverse sequences were assembled using Geneious R11
Thi Mai Linh Le,
Huu Tien Nguyen,
Thi Duyen Nguyen,
Quang Phap Trinh
Journal of Nematology, Volume 52 , 1–4
research-article | 30-November-2018
(Majd Taheri et al., 2013). Those species have been studied by morphological characters except for two unknowns which have been studied by morphological and molecular DNA barcoding using 28S rDNA (Majd Taheri et al., 2013). Root-lesion nematodes, Pratylenchus (Filipjev, 1936), are after root-knot and cyst nematodes listed as the third economically most important genus that adversely affects crop production worldwide (Castillo and Vovlas, 2007; Jones et al., 2013). Pratylenchus hippeastri, the
Ebrahim Shokoohi,
Joaquín Abolafia,
Phatu William Mashela,
Nafiseh Divsalar
Journal of Nematology, Volume 51 , 1–26
research-article | 28-April-2020
microscopy (LM) and scanning electron microscopy (SEM). Additionally, molecular data of this species based in the D2-D3 region of the 28 S rDNA, 18 S rDNA, and internal transcribed spacer (ITS) regions of rDNA genes are included to support the morpho-taxometrical studies. This is the first molecular study of this species and its first valid report from India.
Materials and methods
Nematode isolation, culture, and processing
Soil samples were collected from agricultural farmlands in Mawana, Meerut (28°9
Aasha Rana,
Aashaq Hussain Bhat,
Suman Bhargava,
Ashok Kumar Chaubey,
Joaquín Abolafia
Journal of Nematology, Volume 52 , 1–21
research-article | 03-August-2021
bacterial communities were screened by 16S rDNA sequencing in the four common species of jellyfish including Phyllorhiza punctata, Cyanea capillata, Chrysaora melanaster and Aurelia coerulea, to evaluate the diversity and richness as well as their potential functions involving the life of the four different jellyfish species.
Experimental
Materials and Methods
Jellyfish samples. Individuals of four jellyfish species (P. punctata, C. capillata, C. melanaster, and A. coerulea) were collected alive from
QING LIU,
XINTONG CHEN,
XIAOYA LI,
JIANPING HONG,
GUIXIAN JIANG,
HONGYU LIANG,
WENWEN LIU,
ZHENG XU,
JING ZHANG,
WEI WANG,
LIANG XIAO
Polish Journal of Microbiology, Volume 68 , ISSUE 4, 465–476
research-article | 30-November-2020
in 15 µl TE buffer (10 mM Tris-Cl, 0.5 mM EDTA; pH 9.0, Qiagen) (four DNA samples were prepared for each species) after their examination on temporary slides. DNA samples were stored at ‒20°C until used as PCR templates. Partial sequence of the SSU rDNA gene was amplified using primers 988F (5′-CTCAAAGATTAAGCCATGC-3′), 1912R (5′-TTTACGGTCAGAACTAGGG-3′), 1813F (5′-CTGCGTGAGAGGTGAAAT-3′) and 2646R (5′-GCTACCTTGTTACGACTTTT-3′) with resulting PCR products ranging from 890 to 930 and 970 to 1,017 bp
Parnaz Mortazavi,
Fariba Heydari,
Joaquín Abolafia,
Pablo Castillo,
Majid Pedram
Journal of Nematology, Volume 53 , 1–14
research-article | 01-October-2021
, Progen Scientific, London, UK). The bands were stained with 1.25 µl RedSafe (20,000x) previously added to the agarose gel solution (25 ml). The sequencing reactions of the PCR products were performed at Sistemas Genómicos (Paterna, Valencia, Spain) according the Sanger et al. (1977) method. The DNA sequences obtained for P. pycnus (MZ656001 for the 18S rDNA and MZ656000 for the 28S rDNA) and Tarantobelus arachnicida Abolafia and Peña-Santiago, 2018 (MZ655998–MZ655999 for the 18S rDNA and MZ656002
Joaquín Abolafia,
Matteo Vecchi
Journal of Nematology, Volume 53 , 1–20
Research Article | 03-September-2018
stomatal opening formed from four flaps; greatly expanded labial disc; and eight-sectored annule-like column supporting the labial disc. Thirteen nematodes from various hosts were sequenced for 28S LSU rDNA and compared with other millipede-inhabiting nematodes. Stauratostoma shelleyi is the sister group to the few Thelastoma spp. that have been molecularly characterized using the D2–D3 expansion segments of the 28S LSU rDNA.
Gary Phillips,
Robert J. Pivar,
Xiocaun Sun,
John K. Moulton,
Ernest C. Bernard
Journal of Nematology, Volume 50 , ISSUE 2, 133–146
Research Article | 31-May-2018
In a search for an entomopathogenic nematode to control cranberry insect pests, three Oscheius populations (Rhabditidae) were recovered through the Galleria-bait method from one sample taken in a wild cranberry marsh in Jackson County, Wisconsin, USA. Morphological studies with light microscopy and scanning electron microscopy, as well as molecular analyses of the near-full-length small subunit rDNA gene, D2/D3 expansion segments of the large subunit rDNA gene, internal transcribed spacer, and
Weimin Ye,
Shane Foye,
Ann E. MacGuidwin,
Shawn Steffan
Journal of Nematology, Volume 50 , ISSUE 1, 9–26
research-article | 30-November-2019
. A1 light microscope equipped with a Zeiss Axiocam ERc5s digital camera. For molecular characterization, the 5′-end region of 28S rDNA was amplified using DP391/501 primers (5′-AGCGGAGGAAAAGAAACTAA-3′/5′-TCGGAAGGAACCAGCTACTA-3′) following Nguyen et al. (2019b). Forward and reverse sequences were assembled and analyzed using Geneious R11 (Nguyen et al., 2019b, 2019c). The best fit model was chosen using Mega 7 following Nguyen et al. (2019b).
Results and discussion
Measurements
Eight females: L
Huu Tien Nguyen,
Thi Duyen Nguyen,
Thi Mai Linh Le,
Quang Phap Trinh
Journal of Nematology, Volume 52 , 1–4
research-article | 30-November-2019
) buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0, Qiagen) on a clean slide, and squashed using a clean slide cover with the aid of a pipette tip. The suspension was collected by adding 20 μl of TE buffer after gently removing the slide cover and leaving the solution on the slide (Pedram, 2017). The DNA sample was stored at −20°C until used as the polymerase chain reaction (PCR) template. The near-full-length sequence of the small subunit ribosomal DNA (SSU rDNA) was amplified using the forward primer 18S4
Farahnaz Jahanshahi Afshar
Journal of Nematology, Volume 52 , 1–7
research-article | 30-November-2019
species of Deladenus was recovered from a deadwood sample of a dead forest tree collected from the forests of Golestan province, northern Iran. Thus, the present paper aims to describe the newly recovered species and resolve its phylogenetic relationships with other relevant species and genera using three SSU, LSU rDNA, and COI mtDNA markers.
Materials and methods
Sampling, nematode extraction, mounting, and drawing
Specimens of Deladenus brevis n. sp. were obtained from the bark and rotten wood
Fariba Heydari,
Joaquín Abolafia,
Majid Pedram
Journal of Nematology, Volume 52 , 1–13
research-article | 30-November-2020
verify the amplification using an electrophoresis system (Labnet Gel XL Ultra V–2, Progen Scientific, London, UK). The bands were stained with RedSafe (20,000x) previously added to the agarose gel solution. The sequencing reactions of the PCR products were performed at Sistemas Genómicos (Paterna, Valencia, Spain) according the Sanger et al. (1977) method. The rDNA sequences obtained for Spinocephalus tessellatus n. gen., n. sp. were submitted to the GenBank database.
Phylogenetic analyses
For
Joaquín Abolafia,
Manouchehr Hosseinvand,
Ali Eskandari
Journal of Nematology, Volume 53 , 1–16
research-article | 11-March-2021
South Africa (Van den Berg and Heyns, 1973; Van den Berg et al., 2013).
The present paper reports S. brachyurus from natural areas of South Africa. The aims of the study were (1) to study new populations of S. brachyurus using morphology, and (2) to study the phylogenetic position of South African S. brachyurus using 28 S rDNA and mtDNA.
Materials and methods
Nematode extraction and processing
Rhizosphere soil samples were collected from the natural grass from North West and Limpopo provinces of
Ebrahim Shokoohi
journal of nematology, Volume 53 , 1–13
research-article | 30-November-2020
Tanha Maafi et al. (2003), and used as template for polymerase chain reaction (PCR). The D2-D3 expansion segments of 28S rDNA were amplified using the forward D2A (5′-ACAAGTACCGTGAGGGAAAGTTG-3′) and reverse D3B (5′-TCGGAAGGAACCAGCTACTA-3′) primers (Nunn, 1992). Each PCR reaction mixure with a final volume of 30 μl, contained: 15 μl Taq DNA Polymerase 2x Master Mix RED (Ampliqon, Denmark), 1 μl (10 pmol μl−1) of each forward and reverse primers, 2 μl of DNA template and 11 μl deionised water
Manouchehr Hosseinvand,
Ali Eskandari,
Joaquín Abolafia,
Reza Ghaderi
journal of Nematology, Volume 53 , 1–10
Article | 21-July-2017
sequences of 28S rDNA D2/D3 and internal transcribed spacer 1 (ITS1) fragments. Compared to Enchodorus neodolichurus, it has basic differences in tail characters and spicule lengths. Molecular phylogenetic studies using partial sequences of 28S rDNA D2/D3 fragment of the new species and available sequences of Nordiidae members and several other dorylaim species/genera, revealed E. yeatsi n. sp. and E. dolichurus forming a clade with 0.81 Bayesian posterior probability (BPP). This
MAJID PEDRAM
Journal of Nematology, Volume 49 , ISSUE 1, 21–26
research-article | 30-November-2020
containing 25.65 μl ddH2O, 2.85 μl 10 × PCR buffer and 1.5 μl proteinase K (600 μg/ml) (Promega, Benelux, the Netherlands). The tubes were incubated at −80°C (1 hr), 65°C (1 hr) and 95°C (15 min). Each sample was regarded as an independent DNA sample and stored at −20°C until used as polymerase chain reaction (PCR) template. Primers for 28S rDNA D2-D3 amplification/sequencing were forward primer D2A (5´-ACAAGTACCGTGAGGGAAAGTTG-3´) and reverse primer D3B (5´-TCGGAAGGAACCAGCTACTA-3´) (Nunn, 1992). The 25
Nasir Vazifeh,
Gholamreza Niknam,
Habibeh Jabbari,
Arezoo Naghavi,
Reyes Peña-Santiago
Journal of Nematology, Volume 53 , 1–12
research-article | 30-November-2018
transferred to a small drop of TE buffer (10 mM Tris-Cl, 0.5 mM EDTA; pH 9.0, QIAGEN Inc., Valencia, CA) individually on separate clean slides, and each specimen was squashed using a clean slide cover glass. The suspension was collected by adding 50 μl TE buffer. Each sample was regarded as an independent DNA sample, and stored at −20°C until used as polymerase chain reaction (PCR) template. Primers used for the PCR amplification of the D2–D3 expansion domains of the LSU rDNA were forward D2A (5
Mazdosht Giti,
Leila Kashi,
Majid Pedram
journal of nematology, Volume 51 , 1–11
Article | 24-July-2017
of small subunit (SSU) and large subunit (LSU) rDNA D2/D3 fragments, the new species formed a clade with two currently available GenBank-derived, unspecified isolates/sequences in SSU and three other isolates/sequences in LSU trees, respectively.
MAJID PEDRAM
Journal of Nematology, Volume 49 , ISSUE 2, 223–230
Research Article | 31-May-2018
Three populations of neotylenchid nematodes were isolated in Ningbo, P. R. China, from white pine lumber (Pinus monticola) imported from the USA. The nematodes were morphologically intermediate between Hexatylus and Deladenus. The nematodes were molecularly characterized based on sequences of the rDNA small subunit 18S, large subunit 28S D2/D3, and internal transcribed spacer sequences. The phylogenetic inferences placed the nematodes with other neotylenchid nematodes, i.e., Fergusobia and
Qing Yu,
Maria Munawar,
Jianfeng Gu,
Weimin Ye
Journal of Nematology, Volume 50 , ISSUE 1, 69–76
research-article | 30-November-2020
adding 15 μl TE buffer. The DNA sample was stored at −20°C. Primers for 28S rDNA D2-D3 amplification/sequencing were forward primer D2A (5´-ACAAGTACCGTGAGGGAAAGT-3´) and reverse primer D3B (5´-TCGGAAGGAACCAGCTACTA-3´) (Nunn, 1992). The PCR cycles and sequencing of amplified fragments were according to Jahanshahi Afshar et al. (2019) and sequenced directly for both strands using the same primers with an ABI 3730XL sequencer (Bioneer Corporation, South Korea). The newly generated sequence for the new
Fariba Heydari,
Mohammad Reza Atighi,
Ebrahim Pourjam,
Majid Pedram
Journal of Nematology, Volume 53 , 1–11
research-article | 30-November-2019
followed as described by Tanha Maafi et al. (2003). Fragments of D2-D3 expansion segments of 28 S rDNA were amplified using the forward D2A (5’–ACAAGTACCGTGAGGGAAAGT–3’) and reverse D3B (5’–TCGGAAGGAACCAGCTACTA–3’) primers (Nunn, 1992). The 30 μl PCR contained 15 μl Taq DNA Polymerase 2 × MasterMix (Ampliqon, Denmark), 1 μl (10 pmol μl−1) each of forward and reverse primers, 2 μl of DNA template and 11 μl deionised water. This mixture was placed into a Hybaid Express thermal cycler (Hybaid, Ashford
Manouchehr Hosseinvand,
Ali Eskandari,
Reza Ghaderi
Journal of Nematology, Volume 52 , 1–10
Original Paper | 30-June-2018
A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp
MATEJ REMENÁR,
ANNA KAMLÁROVÁ,
JANA HARICHOVÁ,
MARCEL ZÁMOCKÝ,
PETER FERIANC
Polish Journal of Microbiology, Volume 67 , ISSUE 2, 191–201
Article | 21-July-2017
isolates possess six ridges in their lateral field instead of eight reported in the original description. The analysis of ITS-rDNA sequences revealed nucleotide differences at 345, 608, and 920 positions in aligned data. No difference was observed in D2-D3 domain. The S. surkhetense COI gene was studied for the first time as well as the molecular characterization of their Xenorhabdus symbiont using the sequences of recA and gyrB genes revealing Xenorhabdus stockiae as its symbiont
AASHIQ HUSSAIN BHAT,
I STKHAR,
ASHOK KUMAR CHAUBEY,
VLADIMIR PUZA,
ERNESTO SAN-BLAS
Journal of Nematology, Volume 49 , ISSUE 1, 92–102
research-article | 16-January-2021
segments of the 18 S, ITS1, 5.8 S, ITS2, and 28 S regions of the ribosomal DNA array (rDNA) and mitochondrial DNA (mtDNA) have proved to be efficient diagnostic tools for accurately identifying of RKNs (Landa et al., 2008; Naz et al., 2012).
Accurate identification of M. graminicola, as well as its prevalence and distribution spectra, is fundamental for applying management strategies in the field. Therefore, we used morphological and molecular approaches to identify RKNs in order to determine the
Abdul Jabbar,
Nazir Javed,
Anjum Munir,
Huma Abbas,
Sajid A. Khan,
Anam Moosa,
Muhammad Jabran,
Byron J. Adams,
Muhammad A. Ali
Journal of Nematology, Volume 52 , 1–17
Research Article | 03-December-2018
L. K. Carta,
S. Li
Journal of Nematology, Volume 50 , ISSUE 4, 533–542
research-article | 30-November-2020
. The specimens were then transferred to two individual Eppendorf tubes containing 15 µl ddH2O and their respective DNA was extracted using the chelex-100 protocol of Rashidifard et al. (2019). The DNA samples were stored at –20°C until used for amplification. The partial sequences of the large subunit ribosomal DNA (LSU rDNA D2-D3) were amplified using forward primer D2A (5′–ACAAGTACCGTGAGGGAAAGT–3′) and reverse primer D3B (5′–TCGGAAGGAACCAGCTACTA–3′) (Nunn, 1992). The polymerase chain reaction (PCR
Farahnaz Jahanshahi Afshar,
Milad Rashidifard,
Joaquín Abolafia,
Miloslav Zouhar,
Hendrika Fourie,
Majid Pedram
Journal Of Nematology, Volume 53 , 1–14
Research Article | 03-September-2018
. sturhani. The morphological differences of the new species with the aforementioned species are discussed. For all the aforementioned species (except L. protae, currently lacking molecular data) the differences of the new species was also confirmed with differences in molecular sequences of D2-D3 expansion domains of 28S rDNA and the corresponding phylogenetic analyses. The partial sequence of the internal transcribed spacer 1 (ITS1) of the new species was also used in phylogenetic analyses. In partial
Farshad Gharibzadeh,
Ebrahim Pourjam,
Majid Pedram
Journal of Nematology, Volume 50 , ISSUE 2, 207–218
research-article | 16-April-2019
phylogenetic tree (Fig. 5).
Phylogenetic analyses
The newly obtained sequences were aligned using MEGA6 (Tamura et al., 2013) and compared with other Xiphinema D2–D3 expansion segment of 28S rDNA gene sequences available in GenBank using the Nblast homology search program. Longidorus helveticus (Lamberti et al., 2001) (AY601566) was chosen as out group. The best-fitted model of DNA evolution was obtained using MrModeltest 2.3 (Nylander, 2004) with the Akaike Information Criterion (AIC). Phylogenetic
Nasir Vazifeh,
Gholamreza Niknam,
Habibeh Jabbari,
Arezoo Naghavi
Journal of Nematology, Volume 51 , 1–17
research-article | 25-May-2020
specimen of the recovered species was picked out, examined on a temporary slide and transferred to a small drop of TE buffer (10 mMTris-Cl, 0.5 mM EDTA, pH 9.0; Qiagen) on a clean slide and crushed using a cover slip. The suspension was collected by adding 20 μl TE buffer. The DNA sample was stored at −20°C until used as PCR template (two separate females were used for this purpose, and two DNA samples were prepared). The SSU rDNA was amplified using the forward primer F22 (5´-TCCAAGGAAGGCAGCAGGC-3
Fariba Heydari,
Majid Pedram
Journal of Nematology, Volume 52 , 1–12
research-article | 30-March-2020
. To prepare DNA extracts, frozen nematodes were thawed, 1 µl proteinase K (from 2 mg/ml stock solution) was added, and the tubes were incubated at 60°C for 60 min, followed by 95°C for 15 min to deactivate the proteinase K. Two or five microliters of extract were used for each PCR reaction.
PCR amplification and cloning
ITS: Amplification of the internal transcribed spacer region ITS1&2 rDNA contained 0.2 µM each primer, TW81 (Joyce et al., 1994) and AB28 (Howlett et al., 1992), 1.5 mM MgCl2
Andrea M. Skantar,
Zafar A. Handoo,
Mihail R. Kantor,
Lynn K. Carta,
Jamal Faghihi,
Virginia Ferris
Journal of Nematology, Volume 52 , 1–8
Original Paper | 10-December-2018
of the following rDNA regions: ITS1, ITS2, 5.8S, 28S rDNA, LSU and β-tubulin were carried out for the isolates studied. A high level of similarity was found between sequences from certain rDNA regions, i.e. ITS1-5.8S-ITS2 and LSU, what confirmed the classification of the isolates to the species A. penicillioides. The classification of our isolates to A. penicillioides species was confirmed also by the phylogenetic analysis.
EULALIA MACHOWICZ-MATEJKO,
AGNIESZKA FURMAŃCZYK,
EWA DOROTA ZALEWSKA
Polish Journal of Microbiology, Volume 67 , ISSUE 4, 407–416
research-article | 30-November-2019
, the mixture was incubated at room temperature (23 ± 2°C) for 10 min and then at 95°C for 3 min. Finally, 20 µL of neutralization solution was added to the tube and vortexed briefly. This DNA extract was stored at −20°C and used as DNA template for PCR reactions in 2 µL aliquots. Three primer pairs targeting 18S rDNA (360F/932R), 28S rDNA (D2A/D3B) and ITS1 rDNA (BL18/5818) (Riga et al., 2007; Duarte et al., 2010; Ye et al., 2015) were used in singleplex PCR (Hajihassani et al., 2018a). The
Ganpati B. Jagdale,
Fereidoun Forghani,
Katherine Martin,
Abolfazl Hajihassani,
Alfredo Dick Martinez-Espinoza
Journal of Nematology, Volume 52 , 1–3
research-article | 30-November-2020
observed by electrophoresis revealed the phenotype VS-1 (G1) (Rm = 0.70) typical of M. graminicola (Carneiro et al., 1996). The sequences of the rDNA regions (ITS: 433 bp and D2-D3 of 28S: 446 bp) were submitted to GenBank (ITS: MW537706 and D2-D3 of 28S: MW537709). Searches on BLAST showed 99 to 100% identity with sequences of M. graminicola isolates from Brazil, Taiwan, and China.
To satisfy a modified Koch’s postulates, J. microcephalus plantlets were grown in 1.7 L pots filled with a sterilized
Cristiano Bellé,
Paulo Sergio dos Santos,
Tiago Edu Kaspary
Journal of Nematology, Volume 53 , 1–4
Research Article | 03-December-2018
Juvenile, female and male nematodes were discovered in wood chips of white pine Pinus strobus from Ashley Falls, MA. Initial observations suggested these nematodes might be PWN, but closer morphological and molecular characterization proved otherwise. Comparison of measured features with those in the literature indicated this nematode population had some unique characteristics. The specimens were identified as Bursaphelenchus antoniae Penas et al., 2006 based on 18S rDNA molecular sequence vs
Lynn K. Carta,
R. L. Wick
Journal of Nematology, Volume 50 , ISSUE 4, 473–478
research-article | 30-November-2020
″) (De Ley et al., 1999), were used in the PCR reactions for partial amplification of the 18S and 28S rDNA region, respectively. PCR was conducted with 8 μl of the DNA template, 12.5 μl of 2X PCR Master Mix Red (Promega, USA) for the Botswanan specimens, 1 μl of each primer (10 pmol μl−1), and ddH2O for a final volume of 30 μl. The amplification was processed using an Eppendorf master cycler gradient (Eppendorf, Hamburg, Germany), with the following program: initial denaturation for 3 min at 94°C, 37
Ebrahim Shokoohi
Journal of Nematology, Volume 53 , 1–5
Original Research | 11-December-2017
and diagnostic features of Pseudacrobeles species and molecular sequence data from the D2-D3 regions of the 28S ribosomal DNA (rDNA) and ITS1-5.8S-ITS2 region of rDNA from the new species, which can be used as molecular barcode sequences.
Jiyeon Kim,
Taeho Kim,
Joong-Ki Park
Journal of Nematology, Volume 49 , ISSUE 2, 162–167
research-article | 30-November-2020
species was characterized using both morphological and molecular techniques, its phylogenetic relationships are also discussed based on 18 S and 28 S rDNA genes.
Materials and methods
Nematode extraction and processing
Prionchulus jonkershoekensis n. sp. specimens were extracted from leaf-litter samples collected from one locality in the Jonkershoek Mountains by using the Baermann tray method (Hooper and Evans, 1993). Nematodes were heat-killed and fixed using the glycerol-ethanol method of
Candice Jansen van Rensburg,
Hendrika Fourie,
Samad Ashrafi,
Milad Rashidifard
Journal of Nematology, Volume 53 , 1–10
research-article | 30-November-2020
same species) controls were performed. All the treatments were replicated 30 times for each combination of the nematode species and observed for 20 consecutive days at 17.5°C.
Molecular characterization and phylogenetic analysis
DNA was extracted from three single virgin first-generation females of nematodes using a DNeasy Blood and Tissue Kit (Qiagen, Germany). PCR amplification of the internal transcribed spacer (ITS) region of rDNA, the D2D3 region of 28 S rDNA, and the mitochondrial cox1 gene
Magdalena Lis,
Ewa Sajnaga,
Marcin Skowronek,
Adrian Wiater,
Kamila Rachwał,
Waldemar Kazimierczak
Journal of Nematology, Volume 53 , 1–24
Article | 03-December-2017
EMMANUEL A. TZORTZAKAKIS,
CAROLINA CANTALAPIEDRA-NAVARRETE,
PABLO CASTILLO,
JUAN E. PALOMARES-RIUS,
ANTONIO ARCHIDONA-YUSTE
Journal of Nematology, Volume 49 , ISSUE 3, 233–235
research-article | 24-November-2020
diagnosis is gaining more reliability for precise and accurate identification of cyst-forming nematodes (Peng et al., 2003). The internal transcribed spacer region of the ribosomal DNA (ITS-rDNA), the D2 and D3 expansion fragments of the 28S ribosomal DNA genes (D2-D3 of 28S-rDNA), and mitochondrial DNA (COI gene) units are good candidate genes for molecular taxonomic and phylogenetic studies (Subbotin et al., 2001; Subbotin et al., 2006; Madani et al., 2004; Vovlas et al., 2017). Based on
Wenhao Li,
Huixia Li,
Chunhui Ni,
Deliang Peng,
Yonggang Liu,
Ning Luo,
Xuefen Xu
Journal of Nematology, Volume 52 , 1–16
research-article | 30-November-2018
Zeiss Axio Lab.A1 light microscope. Measurements and pictures were taken using a ZEN lite software on ZEISS Axiocam ERc5s digital camera (Nguyen et al., 2017).
For molecular studies, Primers D2A (5′-ACAAGTACCGTGGGGAAA GTTG-3′) and D3B (5′-TCGGAAGGAACCAGCTAC TA-3′) were used to amplify D2D3 of 28S rDNA region (Nguyen et al., 2017). Obtained sequence was used for a Blast search in GenBank (Altschul et al., 1997). The data set was analyzed using maximum likelihood (ML) method in MEGA 6 program with
Thi Duyen Nguyen,
Huu Tien Nguyen,
Thi Mai Linh Le,
Thi Tuyet Thu Tran,
Neriza Nobleza,
Quang Phap Trinh
Journal of Nematology, Volume 51 , 1–4
Article | 04-December-2017
monodelphic-prodelphic reproductive system, 15 to 19 mm long conical tail with broad rounded tip, and males absent. The new species is compared with two known species of the genus, Anguillonema poligraphi and A. crenati. Molecular phylogenetic studies of the new species using partial sequences of small subunit (SSU) rDNA revealed that it forms a clade with an unidentified nematode species and two species of the genus Howardula. In phylogenetic analyses using partial sequences of the 28S rDNA (D2-D3
MAHYAR MOBASSERI,
MAJID PEDRAM,
EBRAHIM POURJAM
Journal of Nematology, Volume 49 , ISSUE 3, 286–294
research-article | 30-November-2020
length of stylet, tail and hyaline tail in second-stage juvenile, and the surface differentiation in eggs (Subbotin et al., 2010). However, traditional identification of cyst forming nematode based on morphology is imprecise and time-consuming to separate the related species. During the past 30 years, molecular data, including ITS-rDNA, D2-D3 region of 28S-rDNA, are more accurate tool for identification of cyst-forming nematode species. Sequence analysis of the ITS-rDNA and the D2-D3 region of 28S
Wenhao Li,
Huixia Li,
Chunhui Ni,
Mingming Shi,
Xuejuan Wei,
Yonggang Liu,
Yiwen Zhang,
Deliang Peng
Journal of Nematology, Volume 53 , 1–15
research-article | 30-November-2019
were prepared according to Taylor and Netscher (1974). The determination of the esterase profile was made according to Carneiro and Almeida (2001), using 20 female.
For molecular identification, the D2 to D3 region of 28S rDNA segment was amplified and sequenced using the primers D2A (5′-ACAAGTACCGTGAGGGAAAGTTG-3′) and D3B (5′-TCGGAAGGAACCAGCTACTA-3′) (De Ley et al., 1999) and ITS primers with VRAIN2F (5′-CTTTGTACACACCGCCCGTCGCT-3′) and VRAIN2R (5′-TTTCACTCGCCGTTACTAAGGGAATC-3′) (Vrain et al., 1992
Francisco Jorge Carlos Souza Junior,
Mayara Castro Assunção
Journal of Nematology, Volume 52 , 1–4
research-article | 13-April-2020
supported clade of S. caprifici. This is the first molecular phylogenetic study of the species from Iran, showing D2-D3 sequences of the studied Iranian population is identical to those of the majority of previously sequenced populations.
Figure 1:
Bayesian 50% majority rule consensus tree inferred from D2-D3 large subunit (LSU) rDNA gene sequences of Iranian population of Schistonchus caprifici (Gasparrini, 1864) Cobb, 1927 under the GTR + I + G model. The newly generated sequences are in bold font
Hadi Karimipour Fard,
Hamid Zare
Journal of Nematology, Volume 52 , 1–3
research-article | 30-November-2018
regions of the large subunit ribosomal genes (28S), which is thought to evolve slowly, have been used to examine the evolutionary relationships among species of many genera including Pratylenchus (Al-Banna et al., 1997).
Pratylenchus teres, which was previously considered to be endemic to Western Australia, has recently been re-described as Pratylenchus quasitereoides using traditional methods and sequences of the 28S-D3 region of the rDNA (Hodda et al., 2014). The latter species is reported to occur
Farhana Begum,
John Fosu-Nyarko,
Shashi Sharma,
Bill Macleod,
Sarah Collins,
Michael G. K. Jones
Journal of Nematology, Volume 51 , 1–15
research-article | 17-March-2020
through molecular phenotyping is required to be certain.
Molecular profiles and phylogenetic relationships
The primer pairs D2A/D3B and 26S/V5367 were used to amplify the D2-D3 region of the 28S and rDNA-ITS gene sequences of root-knot nematodes in the Guangdong, Guangxi, and Hunan province of China. The amplified products were 765 bp and 715 bp, respectively. The sequence of the amplified product was submitted to GenBank for a BLAST search, and the results revealed the highest similarity (99-100
Pan Zhang,
Hudie Shao,
Chunping You,
Yan Feng,
Zhenwen Xie
Journal of Nematology, Volume 52 , 1–8
Original Paper | 26-August-2016
Wael S. El-Sayed
Polish Journal of Microbiology, Volume 65 , ISSUE 3, 341–352
research-article | 30-November-2020
identification of specimens from the population of Pratylenchus was carried out by amplifying and sequencing the regions ITS primers with VRAIN2F (5´-CTTTGTACACACCGCCCGTCGCT-3´) and VRAIN2R (5´-TTTCACTCGCCGTTACTAAGGGAATC-3´) (Vrain et al., 1992) and D2-D3 of 28S rDNA segment with the primers D2A (5´-ACAAGTACCGTGAGGGAAAGTTG-3´) and D3B (5´-TCGGAAGGAACCAGCTACTA-3´) (De Ley et al., 1999).
The consensus sequences were formed from the forward and reverse sequences, using the Staden package (Staden et al., 1998
Francisco Jorge Carlos Souza Junior,
Mayara Castro Assunção
Journal of Nematology, Volume 53 , 1–5
Original Paper | 28-June-2017
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soilcontaminated with low concentration of arsenic was dominated by both
Semanti Basu,
Tanima Paul,
Priya Yadav,
Abhijit Debnath,
Keka Sarkar
Polish Journal of Microbiology, Volume 66 , ISSUE 2, 209–221
research-article | 24-April-2019
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, Volume 51 , 1–20
original-paper | 28-March-2019
restriction analysis of the amplified product. These genes are conserved among bacteria but show small variations that allow LAB species identification (Mohania et al. 2008). Using ARDRA of 16S rDNA it is possible to differentiate the main LAB present in wine fermentation (Rodas et al. 2003), but to ensure the identification many authors have used the sequencing of the complete 16S rDNA gene (Reginensi et al. 2013). Although the sequencing of 16S rRNA genes is still considered the gold standard for
JOHANNA SÁNCHEZ,
CARLOS VEGAS,
AMPARO IRIS ZAVALETA,
BRAULIO ESTEVE-ZARZOSO
Polish Journal of Microbiology, Volume 68 , ISSUE 1, 127–137
Research Article | 26-September-2018
SOLOMIA SUSULOVSKA,
PABLO CASTILLO,
ANTONIO ARCHIDONA-YUSTE
Journal of Nematology, Volume 49 , ISSUE 4, 396–402
research-article | 31-August-2020
length: 60.2 ± 5.0 (55.5-67.7) μm, ABW = 16.5 ± 2.5 (13.4-20.1) μm. These morphological characteristics matched with Ditylenchus destructor by Thorne. (Thorne, 1945).
DNA of single nematode (n = 5) was isolated using the Proteinase K method (Kumari and Subbotin, 2012) and amplification of rDNA-ITS region and D2/D3 fragments of the 28S rDNA sequencing were performed with the universal primers 18S (5′-TTGATTACGTCCCTGCCCTTT-3′) and 26S (5′-TTTCACTCGCCGTTACTAAGG-3′) (Vrain et al., 1992). D2A (5
Chunhui Ni,
Shuling Zhang,
Huixia Li,
Yonggang Liu,
Wenhao Li,
Xuefen Xu,
Zhipeng Xu
Journal of Nematology, Volume 52 , 1–2
research-article | 26-March-2021
al., 2006). Following DNA extraction, the polymerase chain reaction (PCR) was carried out using an Eppendorf Mastercycler gradient thermal cycler (Eppendorf, Hamburg, Germany); more details are provided in Table 1. The amplification tube contained 12.5 μl master mix (Promega Corporation, USA), 1 μl of each of the primers (i.e. forward and reverse), 5 μl DNA, and 5.5 μl ddH2O.
Table 1.
Polymerase chain reaction steps used for amplification of the SSU and LSU rDNA genes.
35 cycles
Chantelle Girgan,
Gerhard Du Preez,
Hendrika Fourie,
Milad Rashidifard
Journal of Nematology, Volume 53 , 1–12
research-article | 30-November-2018
Donald Riascos-Ortiz,
Ana Teresa Mosquera-Espinosa,
Francia Varón De Agudelo,
Claudio Marcelo Gonçalves de Oliveira,
Jaime Eduardo Muñoz-Flórez
Journal of Nematology, Volume 51 , 1–13
research-article | 17-March-2020
the Proteinase K method (Kumari and Subbotin, 2012), and the internal transcribed spacer1 (ITS1) region of rDNA and D2/D3 fragments of the 28 S rRNA were amplified with universal primers rDNA2 and rDNA1.58 s (Szalanski et al., 1997), D2A and D3B (Castillo et al., 2003), respectively. PCR products were sequenced by Tsingke Biological Technology (Beijing, China). The ITS1 sequence (MN757910, 721 bp) and D2/D3 sequence (MN757911, 802 bp) were submitted to GenBank and compared with published sequences
Zhi Peng Xu,
Hui Xia Li,
Yong Gang Liu,
Bao Cang Ren,
Chun Hui Ni,
Jin Hui Ma
Journal of Nematology, Volume 52 , 1–2
Original Paper | 27-September-2017
Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit werecarried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP
Tomasz Cłapa,
Dorota Narożna,
Rafał Siuda,
Andrzej Borkowski,
Marek Selwet,
Cezary J. Mądrzak,
Ewa Koźlecka
Polish Journal of Microbiology, Volume 66 , ISSUE 3, 375–381
research-article | 30-November-2019
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, Volume 52 , 1–5
Research Article | 17-October-2018
segments of 28S rRNA, and ITS1 rDNA were amplified using primer pairs 360F (5′ CTACCACATCCAAGGAAGGC 3′)/932R (5′ TATCTGATCGCTGTCGAACC 3′), D2A (5′ ACAAGTACCGTGAGGGAAAGTTG 3′)/D3B (5′ TCGGAAGGAACCAGCTACTA 3′), and BL18 (5′ CCCGTCGCTACTACCGATT 3′)/5818 (5′ ACGARCCGAGTGATCCAC 3′), respectively (Riga et al., 2007; Duarte et al., 2010; Ye et al., 2015; Shaver et al., 2016). The obtained PCR fragments were purified using QIAquick Gel Extraction Kit (Qiagen Inc., Santa Clara, CA, USA), sequenced and deposited
Abolfazl Hajihassani,
Negin Hamidi,
Bhabesh Dutta,
Chris Tyson
Journal of Nematology, Volume 50 , ISSUE 3, 453–455
Article | 21-July-2017
phylogenetic studies based on partial sequences of 28S rDNA D2/D3 fragments, all species formed a clade with high Bayesian posterior probability in Bayesian inference, indicating the monophyly of the genus. The clade of Coslenchus spp. formed a highly supported monophyletic group, a sister clade to two species of the genus Aglenchus.
YOUSEF PANAHANDEH,
EBRAHIM POURJAM,
MAJID PEDRAM
Journal of Nematology, Volume 48 , ISSUE 4, 268–279
Research Article | 03-December-2018
slender, slightly curved and 17.5 to 18.9 µm long. In the phylogenetic analysis based on 18S, D2-D3 of 28S and ITS regions of rDNA, the new species is clustered with Paratylenchid species having longer stylet length. Morphologically, the new species belongs to Group 9 of Paratylenchus sensu lato and is most similar to G. latescens.
Munawar Maria,
Ruihang Cai,
Weimin Ye,
Thomas O. Powers,
Jingwu Zheng
Journal of Nematology, Volume 50 , ISSUE 4, 611–622
Original Paper | 28-June-2017
The purpose of this study was to determine the antimicrobial activity and occurrence of bacteriocin structural genes in Enterococcus spp. isolated from different cheeses and also investigate some of their virulence factors. Enterococcus strains were isolated from 33 different cheeses. Enterococcus faecium (6 strains) and Enterococcus faecalis (5 strains) enterocin-producing strains were identified by 16S rDNA analyses. Structural genes entA, entB, entP and entX were detected in some isolates
Mine Avci,
Banu Özden Tuncer
Polish Journal of Microbiology, Volume 66 , ISSUE 2, 223–233
research-article | 30-November-2018
D2–D3 expansion segments of LSU rDNA were amplified using the primers D2A and D3B (5′-ACAAGTACCGTGGGGAAAGTTG-3′ and 5′-TCGGAAGGAACCAGCTACTA-3′) (De Ley et al., 1999). The newly obtained sequence was compared with previously submitted sequences into the GenBank database (Altschul et al., 1997) using BLAST search. Multiple alignments were made using MUSCLE and Modeltest was used to select the best fit model in MEGA 6 (Tamura et al., 2013). MrBayes 3.2.6 (Huelsenbeck and Ronquist, 2001) in Geneious
Thi Duyen Nguyen,
Huu Tien Nguyen,
Thi Mai Linh Le,
Neriza Nobleza,
Quang Phap Trinh
journal of nematology, Volume 51 , 1–5
research-article | 30-November-2019
Ovomermis sinensis nematode (scale bar: 1 cm).
Figure 3:
Post-parasitic juvenile Ovomermis sinensis nematode emerging from Spodoptera frugiperda.
Molecular analyses
In the molecular analyses, the two individuals analyzed showed no polymorphism in the 18 S rDNA gene fragment detected (accession number MN367956 and MN367957). The D3 fragment of 28 S rDNA gene was uploaded with accession numbers MN367954 and MN367955. Based on the NJ trees of 18 S and D3 region in 28 S (Figs. 4 and 5
Bingjiao Sun,
Fen Li,
Xiaorui He,
Fengqin Cao,
Elizabeth Bandason,
David Shapiro-Ilan,
Weibin Ruan,
Shaoying Wu
Journal of Nematology, Volume 52 , 1–7
Article | 03-December-2017
The taxonomy and the systematics of the genus Makatinus are discussed by means of the characterization of its morphological pattern and the first molecular (D2–D3 expansion segments of 28S rDNA) analysis of a representative of this taxon, Makatinus crassiformis from Costa Rica. The presence of two or more pairs of male ad-cloacal genital papillae is the most characteristic autapomorphy of the genus, but the status of its species on this concern differ among them. Both morphological and
REYES PENA-SANTIAGO,
INGRID VARELA
Journal of Nematology, Volume 49 , ISSUE 3, 245–253
Original Paper | 26-August-2016
Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole
Mosbah Mahdhi,
Nadia Houidheg,
Neji Mahmoudi,
Abdelhakim Msaadek,
Mokhtar Rejili,
Mohamed Mars
Polish Journal of Microbiology, Volume 65 , ISSUE 3, 331–339
research-article | 30-November-2019
et al., 2004; Paes et al., 2012) (Fig. 4A). Taxonomic identification of M. enterolobii has proved to be very challenging based on only the traditional means and has resulted in incorrect identification and misreporting (Brito et al., 2004). Molecular characterization based on ITS rDNA sequences (NCBI GenBank accession number KT271569) and SCAR marker resulted in authentication of the species (Fig. 4B). In this line, use of molecular markers, viz., ribosomal D2D3 expansion segment, ITS rDNA, IGS
Tushar Manohar Ghule,
Victor Phani,
Vishal Singh Somvanshi,
Maya Patil,
Somnath Bhattacharyya,
Matiyar Rahaman Khan
Journal of Nematology, Volume 52 , 1–9
Short Communication | 28-June-2017
Beata Zimowska,
Ewa Dorota Zalewska,
Ewa Dorota Król,
Agnieszka Furmańczyk
Polish Journal of Microbiology, Volume 66 , ISSUE 2, 281–285
Article | 21-July-2017
-stage juveniles lack a stylet, the pharynx degenerated, and can be differentiated into preadult females and males based on the position of the genital primordia. The third-stage juveniles are similar to females but smaller. Phylogenetic studies using the rDNA small subunit 18S, large subunit 28S D2/D3, and internal transcribed spacer (ITS) sequences collectively provide evidence of a grouping with other Gracilacus and some species of Paratylenchus with stylet length of females longer than 41 mm
QING YU,
WEIMIN YE,
TOM POWERS
Journal of Nematology, Volume 48 , ISSUE 3, 203–213
Research Article | 03-December-2018
juvenile Oscheius rugaoensis (Zhang et al., 2012) Darsouei et al., 2014 (Rhabditidae), and juvenile and adult Mononchoides sp. (Diplogastridae) based on images, morphometrics, and sequences of 18S and 28S rDNA. A novel short 28S sequence of a separate population of Oscheius necromenus SB218 from Australian millipedes was also included in a phylogenetic comparison of what can now be characterized as a species complex of millipede-associated Oscheius. The only other nematode associates of millipedes
L. K. Carta,
W. K. Thomas,
V. B. Meyer-Rochow
Journal of Nematology, Volume 50 , ISSUE 4, 479–486
research-article | 30-November-2018
identical thus only one was included in this study. The resulting D2/D3 rDNA sequence was compared against a set of reference sequences of M. xenoplax selected from GenBank (NCBI) to cover a range of species from Criconematidae. Nucleotide sequences from isolates for which GenBank sequence data were available for the homologous fragment of D2/D3 rDNA gene were retrieved and a new multiple alignment was performed, using ClustalW integrated in software MEGA 6 (Tamura et al., 2013).
A phylogenetic tree was
M. L. Inácio,
L. C. Rusinque,
M. J. Camacho,
F. Nóbrega
Journal of Nematology, Volume 51 , 1–6
Article | 21-July-2017
DNA (rDNA). Phylogenetic data show that S. biddulphi n. sp. belongs to the ‘‘bicornutum’’ clade within the Steinernematidae family.
HARUN CIMEN,
VLADIMI´R PU°zA,
JIRI NERMUT,
JUSTIN HATTING,
TSHIMA RAMAKUWELA,
SELCUK HAZIR
Journal of Nematology, Volume 48 , ISSUE 3, 148–158
Article | 21-July-2017
based on sequences of D2-D3 expansion region of 28S and 18S rDNA, confirmed its status as a new species.
BEHROUZ GOLHASAN,
RAMIN HEYDARI,
MEHRAB ESMAEILI,
ESMAEIL MIRAEIZ
Journal of Nematology, Volume 49 , ISSUE 1, 67–76
Original Paper | 07-June-2016
Two hundred and fifty bacterial strains were isolated from pinyon rhizosphere and screened for biosurfactants production. Among them, six bacterial strains were selected for their potential to produce biosurfactants using two low cost wastes, crude glycerol and lactoserum, as raw material. Both wastes were useful for producing biosurfactants because of their high content in fat and carbohydrates. The six strains were identified by 16S rDNA with an identity percentage higher than 95%, three
Arnoldo Wong-Villarreal,
Lizbeth Reyes-López,
Hipólito Corzo González,
Cristina Blanco González,
Gustavo Yáñez-Ocampo
Polish Journal of Microbiology, Volume 65 , ISSUE 2, 183–189
research-article | 28-April-2020
transferred to an Eppendorf tube containing 25.65 μl ddH2O, 2.85 μl 10 × PCR buffer and 1.5 μl proteinase K (600 μg/ml) (Promega, Benelux, the Netherlands). The tubes were incubated at −80°C (1 h), 65°C (1 h) and 95°C (15 min). The extracted DNA was stored at −20°C until use. The D2-D3 domains of the 28S rDNA were amplified with forward primer D2A (5´-ACAAGTACCGTGAGGGAAAGTTG-3´) and reverse primer D3B (5´-TCGGAAGGAACCAGCTACTA-3´) (Nunn, 1992). In total, 25 μl PCR reaction mixture was prepared constituting
Nasir Vazifeh,
Gholamreza Niknam,
Habibeh Jabbari,
Reyes Peña-Santiago
Journal of Nematology, Volume 52 , 1–12
original-paper | 08-September-2020
rates in PVK liquid medium were 88 mg P/l * d and 115 mg P/l * d for bacterial strains A2 and A3, respectively. Therefore, bacterial strain A3 was selected because it was able to grow with tricalcium phosphate being the only phosphorus source on both solid and liquid media, and it solubilized orthophosphates to a higher rate than bacterial strain A2.
The strain identification based on the 16S rRNA gene sequence. The 16S rDNA sequence was analyzed using the BLASTn algorithm and showed that bacterial
GUSTAVO YAÑEZ-OCAMPO,
MARTHA E. MORA-HERRERA,
ARNOLDO WONG-VILLARREAL,
DENISSE M. DE LA PAZ-OSORIO,
NADIA DE LA PORTILLA-LÓPEZ,
JORGE LUGO,
ROCIO VACA-PAULÍN,
PEDRO DEL ÁGUILA
Polish Journal of Microbiology, Volume 69 , ISSUE 3, 357–365
research-article | 30-November-2019
, PCR reaction, and gel electrophoresis
DNA from previously selected living males and females was extracted using chelex-100 as described by Rashidifard et al. (2019). Polymerase chain reaction (PCR) conditions followed the protocol of Swart et al. (2020) with the following DNA markers used for DNA amplification: 28 S rDNA: D2A (5–ACAAGTACCGTGAGGGAAAGTTG–3), D3B (5–TCGGAAGGAACCAGCTACTA–3) (Subbotin et al., 2006), and 18 S rDNA: SSU F04 (GCTTGTCTCAAAGATTAAGCC), SSU R26 (CATTCTTGGCAAATGCTTTCG
Mariette Marais,
Esther van den Berg,
Hendrika Fourie,
Milad Rashidifard
Journal of Nematology, Volume 52 , 1–12
research-article | 30-November-2020
-D3 of rDNA by Kanzaki and Giblin-Davis (2012) showed four major clades. Based on molecular data, Kanzaki et al. (2014) erected a new subfamily Tylaphelenchinae including Pseudaphelenchus Kanzaki et al., 2009 and Tylaphelenchus Rühm, 1956 assigning them to clade one. Recently, Pedram et al. (2018) added a new genus, Basilaphelnchus Pedram et al., 2018, to this subfamily. They also considered Albiziaphelenchus Bajaj, 2012 as the fourth genus for Tylaphelenchinae. However, molecular data are
Behrouz Golhasan,
Esmaeil Miraeiz,
Zahra Tanha maafi,
Ramin Heydari
Journal of Nematology, Volume 53 , 1–11
Article | 21-July-2017
Sectonema caobangense sp. n. from evergreen forest soil in Vietnam is described, including scanning electron micrograph (SEM) observations and D2-D3 LSU rDNA analysis. The new species is characterized by its 3.12 to 5.80mmlong body, lip region offset by deep constriction and 21 to 23 mm broad, mural tooth 13 to 14 mm long at its ventral side, 940 to 1,112 mm long neck, pharyngeal expansion occupying 61% to 69% of total neck length, uterus a long simple tube-like structure 292 to 363
SERGIO ALVAREZ-ORTEGA,
THI ANH DUONG NGUYEN,
JOAQUI´N ABOLAFIA,
MICHAEL BONKOWSKI,
REYES PEN˜A-SANTIAGO
Journal of Nematology, Volume 48 , ISSUE 2, 95–103
Research Article | 26-September-2018
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, Volume 49 , ISSUE 4, 418–426
Original Paper | 10-December-2018
Abstract
Paeonia ostii is known for its excellent medicinal values as Chinese traditional plant. To date, the diversity of culturable endophytes associated with P. ostii is in its initial phase of exploration. In this study, 56 endophytic bacteria and 51 endophytic fungi were isolated from P. ostii roots in China. Subsequent characterization of 56 bacterial strains by 16S rDNA gene sequence analysis revealed that nine families and 13 different genera were represented. All the fungal strains
RUI-XIAN YANG,
SHAO-WEN ZHANG,
DONG XUE,
JUN-HAO XUAN,
YUAN-BO ZHANG,
BIAO-BIAO PENG
Polish Journal of Microbiology, Volume 67 , ISSUE 4, 441–454
research-article | 02-April-2019
28s rDNA gene (Nunn, 1992). The amplification of near full length 18s rDNA gene was attempted by primers SSU_F_07 (AAAGATTAAGCCATGCATG) and SSU_R_81 (TGATCCWKCYGCAGGTTCAC) (Gutiérrez-Gutiérrez et al., 2012). Each PCR reaction comprised of 1 unit of Platinum Taq polymerase (Invitrogen Carlsbad, CA, USA), 1x Taq polymerase buffer, 0.2 mM dNTPs, 1.5 mM MgCl2, 0.4 µM forward and reverse primers and 6 µl of template DNA. The thermocycling conditions for ITS were – Initial denaturation at 95 °C for 5
Puneet Kumar,
Wajih Jamal,
Vishal S. Somvanshi,
Khushbu Chauhan,
Sabia Mumtaz
Journal of Nematology, Volume 51 , 1–11
research-article | 24-April-2020
). The following primers were used for amplification and sequencing: SSU F04 (GCTTGTCTCAAAGATTAAGCC) and SSU R26 (CATTCTTGGCAAATGCTTTCG) (Blaxter et al., 1998) for SSU rDNA; and D2A (5´-ACAAGTACCGTGAGGGAAAGTTG-3´) and D3B (5´-TCGGAAGGAACCAGCTACTA-3´) (Subbotin et al., 2006) for D2-D3 LSU rDNA.
Four microliters of PCR products were loaded on a 1% agarose gel (40 mMTris, 40 mM boric acid, and 1 mM EDTA) to check the quality of the amplified DNA. The DNA bands were stained with GelRed and visualized and
Milad Rashidifard,
Gerhard Du Preez,
Joaquín Abolafia,
Majid Pedram
Journal of Nematology, Volume 52 , 1–10
research-article | 18-March-2020
(synthesized by Majorbio, Shanghai, China) were used in the PCR analyses to amplify the near full-length SSU and D2-D3 expansion segments of LSU rDNA. The SSU region was amplified as two partially overlapping fragments; for the first fragment, the forward 988F (5′-CTC AAA GAT TAA GCC ATG C-3′) and reverse 1912R (5′-TTT ACG GTC AGA ACT AGG G-3′) primers were used and for the second part, the forward 1813F (5′-CTG CGT GAG AGG TGA AAT-3′) and reverse 2646R (5′-GCT ACC TTG TTA CGA CTT TT-3′) primers were used
Jianfeng Gu,
Munawar Maria,
Lele Liu,
Majid Pedram
Journal of Nematology, Volume 52 , 1–11
research-article | 30-November-2019
: 9.94% in Ischnura fluviatilis and 4.76% in Rhionaeschna bonaerensis.
Specimens deposited: all types have been deposited in the Colección Helmintológica del Museo de Ciencias Naturales de La Plata with the following accession numbers: Holotype male No. MLP-He 7639, allotype female No. MLP-He 7640, and one paratype (postparasitic juvenile) No. MLP-He 7641.
Etymology: this species is named after Enzo Rusconi, nephew of JMR.
DNA characterization and phylogenetic analysis
The 18S rDNA sequence of
José Matias Rusconi,
Cristian Di Battista,
Darío Balcazar,
Matías Rosales,
María Fernanda Achinelly
Journal of Nematology, Volume 52 , 1–9
research-article | 30-November-2020
illustrations were edited by using Adobe Photoshop CC 2018.
DNA extraction, polymerase chain reaction (PCR), and sequencing
Nematode DNA was extracted from a single individual as described by Holterman et al. (2006) and DNA extracts were stored at –20° until used as PCR template. The D2-D3 expansion segment 28S rDNA and 18S were amplified using the forward D2A (5′–ACAAGTACCGTGGGGAAAGTTG–3′) and reverse D3B (5′–TCGG AAGGAACCAGCTACTA–3′) primers (Subbotin et al., 2006) and primers 18S (18F : 5
Tam T. T. Vu,
Thi Mai Linh Le,
Thi Duyen Nguyen
Journal of Nematology, Volume 53 , 1–22
Article | 21-July-2017
, joins together anterior to the spicules, and is partially extended and decorated with microvilli. The spicules are incompletely separated, and the tail does not extend beyond the bursa. Phylogenetic trees of 18S rDNA and internal transcribed spacer indicate that the new species belongs to the insectivora group of the genus Oscheius; it is most closely related to O. myriophilus, and the two species can be distinguished on the basis of their different body length, morphological
GUIXIN ZHOU,
HUAN YANG,
FENG WANG,
HAORAN BAO,
GUOXIANG WANG,
XIANGLONG HOU,
JIAN LIN,
GABRIEL YEDID,
KEYUN ZHANG
Journal of Nematology, Volume 49 , ISSUE 1, 33–41