Molecular and morphological characterisation of Paralongidorus iranicus n. sp. and P. bikanerensis (Lal & Mathur, 1987) Siddiqi, Baujard & Mounport, 1993 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2012 ◽  
Vol 14 (4) ◽  
pp. 427-443 ◽  
Author(s):  
Majid Pedram ◽  
Ebrahim Pourjam ◽  
Somayeh Namjou ◽  
Mohammad Reza Atighi ◽  
Carolina Cantalapiedra-Navarrete ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Large Body ◽  
Original Description ◽  
Phoenix Dactylifera ◽  
Rrna Gene ◽  
28S Rrna ◽  
Northern Iran ◽  
Data Set ◽  
Eastern Iran ◽  
Amphidial Fovea

Paralongidorus iranicus n. sp., a new bisexual species of the genus, is described and illustrated by light microscopy, scanning electron microscopy and molecular studies from specimens collected in the rhizosphere of Scots pine (Pinus sylvestris) from the Caspian (Khazar) seashore, Nour, northern Iran. Paralongidorus iranicus n. sp. is characterised by the large body size (7.8-11.4 mm), a rounded lip region, clearly set off by a collar-like constriction at level of, or slightly posterior to, the amphidial aperture, and bearing a very large, stirrup-shaped, amphidial fovea, with conspicuous slit-like aperture, a very long and flexible odontostyle ca 170 μm long, guiding ring located at 34 μm from anterior end and males with spicules ca 80 μm long. In addition, data from an Iranian population of P. bikanerensis recovered from the rhizosphere of palm (Phoenix dactylifera L.) in Bam, Kerman province, south-eastern Iran, agree very well and are very close to the original description of the species from India. The D2 and D3 expansion regions of 28S rRNA gene, ITS1, and 18S rRNA sequences were obtained for P. iranicus n. sp. and P. bikanerensis. Phylogenetic analyses of P. iranicus n. sp. and P. bikanerensis rRNA gene sequences and of Longidorus spp. sequences published in GenBank were done using Maximum Likelihood and Bayesian inference. Paralongidorus species (including P. iranicus n. sp.) clustered together; however, P. bikanerensis clustered within Longidorus spp. and was clearly separated from all other Paralongidorus spp. in trees generated from the D2-D3 expansion segments of 28S and partial 18S data set, respectively.

Description and molecular characterisation of Paralongidorus litoralis sp. n. and P. paramaximus Heyns, 1965 (Nematoda: Longidoridae) from Spain

Nematology ◽  
2008 ◽  
Vol 10 (1) ◽  
pp. 87-101 ◽  
Author(s):  
Juan E. Palomares-Rius ◽  
Sergei A. Subbotin ◽  
Blanca B. Landa ◽  
Nicola Vovlas ◽  
Pablo Castillo
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Large Body ◽  
Original Description ◽  
The Body ◽  
Southern Spain ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
Data Set

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.

scholarly journals Morphological and molecular characterisation of Paralongidorus plesioepimikis n. sp. (Nematoda: Longidoridae) from southern Spain

Nematology ◽  
2013 ◽  
Vol 15 (3) ◽  
pp. 363-378 ◽  
Author(s):  
Juan E. Palomares-Rius ◽  
Carolina Cantalapiedra-Navarrete ◽  
Carlos Gutiérrez-Gutiérrez ◽  
Gracia Liébanas ◽  
Pablo Castillo
Keyword(s):  
Anterior Part ◽  
Phylogenetic Analyses ◽  
Southern Spain ◽  
Rrna Gene ◽  
28S Rrna ◽  
Data Set ◽  
Cephalic Lobe ◽  
Pharyngeal Gland ◽  
Amphidial Fovea ◽  
Partial 18S

Paralongidorus plesioepimikis n. sp. is described and illustrated by light microscopy, scanning electron microscopy and molecular studies from specimens collected in a sandy soil in the rhizosphere of stone pine (Pinus pinea) in Bonares (Huelva Province), southern Spain. The new species is characterised by a very long body (9.71-14.11 mm), an expanded and rounded lip region, with a clear constriction followed by a depression posterior to the amphidial aperture, a very long and flexible odontostyle (202-227 μm), guiding ring located at 36.5-44.0 μm from anterior end, dorsal pharyngeal gland nucleus in anterior part of bulb, one subventral pair of nuclei near middle of bulb, vulva at 33-38%, and a dorsally convex tail with rounded terminus (32-39 μm long). SEM observations showed a very large amphidial fovea with conspicuous aperture ca three-fourths as wide as lip region and cephalic papillae appearing as small apertures, each located just anterior to a distinct cephalic lobe. The sequences of the D2-D3 expansion segments of 28S rRNA, partial 18S rRNA and ITS rRNA gene for P. plesioepimikis n. sp. were obtained. Phylogenetic analyses of P. plesioepimikis n. sp. rRNA gene sequences and of Paralongidorus spp. and Longidorus spp. sequences published in GenBank were done using Maximum Likelihood and Bayesian inference. Paralongidorus species (including P. plesioepimikis n. sp.) clustered together, except for P. bikanerensis which clustered within Longidorus spp. and was clearly separated from all other Paralongidorus spp. in trees generated from the D2-D3 expansion segments of 28S and partial 18S data set. ML analysis using SH-test for the validity of Paralongidorus was performed and showed the validity of the genus using the D2-D3 expansion segment of 28S and partial 18S.

Morphological and molecular characterisation of Heterodera koreana (Vovlas, Lamberti & Choo, 1992) Mundo-Ocampo, Troccoli, Subbotin, Del Cid, Baldwin & Inserra, 2008 (Nematoda: Heteroderidae) from bamboo in Japan

Nematology ◽  
2017 ◽  
Vol 19 (3) ◽  
pp. 333-350 ◽  
Author(s):  
Shigeyuki Sekimoto ◽  
Taketo Uehara ◽  
Takayuki Mizukubo
Keyword(s):  
Phylogenetic Analyses ◽  
Original Description ◽  
Cyst Nematode ◽  
Soil Samples ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
Phyllostachys Edulis ◽  
Relationship Of ◽  
First Time

The Korean cyst nematode, Heterodera koreana, was recorded for the first time from Japan and characterised morphologically, morphometrically and molecularly. In total, 41 populations were detected from soil samples collected from the rhizosphere of four bamboo species in Japan: 31 populations from moso bamboo (Phyllostachys edulis), seven from madake (P. bambusoides), two from henon bamboo (P. nigra var. henonis) and one from fish pole bamboo (P. aurea). The morphology and morphometrics of the Japanese population were in agreement with those of the original description of H. koreana from South Korea and other subsequent descriptions from China and Iran, with the exception of some minor differences. The results of the phylogenetic analyses of the D2-D3 expansion segments of 28S rRNA gene and ITS rRNA gene sequences confirmed the species identification and phylogenetic relationship of H. koreana with other Heterodera species. The COI mtDNA gene sequences were obtained for the first time for H. koreana. Three COI haplotypes found in Japanese H. koreana populations showed a characteristic geographical distribution in Japan.

Morphological and molecular characterisation of Paralongidorus francolambertii sp. n. (Nematoda: Longidoridae) from Serbia

Nematology ◽  
2017 ◽  
Vol 19 (6) ◽  
pp. 681-695 ◽  
Author(s):  
László Barsi ◽  
Francesca De Luca
Keyword(s):  
Phylogenetic Analyses ◽  
The Body ◽  
Likelihood Method ◽  
Rrna Gene ◽  
28S Rrna ◽  
Sister Relationship ◽  
Large Size ◽  
Tilia Tomentosa ◽  
Amphidial Fovea ◽  
Cuticular Layer

Paralongidorus francolambertii sp. n., a bisexual species found in the rhizosphere of silver lime (Tilia tomentosa) and common juniper (Juniperus communis), is described. The species is characterised by its medium to large size (L = 5.86-8.29 mm) and slender body (a = 143-197), a lip region flattened with rounded profile, clearly offset from the body by a deep constriction, a narrow neck between the head and body, a shoulder-like body posterior to the neck, a stirrup-shaped amphidial fovea, with conspicuous slit-like aperture, lying on the lateral cuticular collar, a moderately long odontostyle ca 140 μm long, a guide ring located at ca 28 μm from anterior end, a tail terminus with thickened outer cuticular layer in both sexes, and males with spicules ca 52 μm long. The D2-D3 expansion domains of the 28S rRNA gene and the ITS-containing region of P. francolambertii sp. n. were amplified and sequenced. Phylogenetic analyses by using the Maximum Likelihood method showed that P. francolambertii sp. n. had a sister relationship with P. rex and that all Paralongidorus species formed a well-supported group.

Morphological and molecular characterisation of populations of Longidorus longicaudatus Siddiqi, 1962 and L. americanus Handoo, Carta, Skantar, Ye, Robbins, Subbotin, Fraedrich & Cram, 2005 from Florida, USA

Nematology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Renato N. Inserra ◽  
Alberto Troccoli ◽  
Silvia Vau ◽  
Sergei A. Subbotin
Keyword(s):  
Gene Sequence ◽  
Original Description ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Pine Needle ◽  
Type Specimens ◽  
Gene Sequence Analysis ◽  
Amphidial Fovea ◽  
Two Populations

Summary Two populations of needle nematode, Longidorus longicaudatus Siddiqi, 1962, are described from Quercus hemisphaerica, Q. nigra and Q. virginiana from north Florida, USA. These populations are characterised morphologically by females having a body shorter than 3800 μm, a rounded or slightly flattened lip region, an amphidial fovea pouch-like often with two symmetrical lobes, an odontostyle 99-110 μm long, a conoid tail ending in a bluntly pointed terminus, ranging values of ratio c′ greater than 2, and males very rare. The polytomous code for these populations is A34, B23, C2, D23, E2, F12, G12, H6, I12, J1, K6. Although the morphology and morphometrics of these two populations fit the original description of Longidorus longicaudatus, Florida specimens have greater diameters of lip region, mid and anal body than those of the five type specimens used for the description of this species. The Florida L. longicaudatus is similar to L. paralongicaudatus, but differs from the paratypes of this species in having smaller and greater values of ratios c (53.8 (43.8-64.5) vs 79.2 (61.9-103.5)) and c′ (2.4 (2.1-2.9) vs 1.8 (1.5-2.0)), respectively, and longer tail (60 (53-67) vs 46 (36-53) μm). Molecular characterisation of one of the two Florida L. longicaudatus populations was made based on the D2-D3 of 28S rRNA, ITS1 rRNA and COI gene sequences. The results of the ITS1 rRNA gene sequence analysis indicated that it is genetically different from L. paralongicaudatus. A few specimens of a needle nematode associated with L. longicaudatus were identified morphologically and molecularly as the pine needle nematode, L. americanus. This detection is a new record of the occurrence of the pine needle nematode in Florida.

Hemicriconemoides phoenicis Van den Berg et al., 2015 (Nematoda: Criconematidae) from Iran: a morphological and molecular phylogenetic study

Nematology ◽  
2020 ◽  
Vol 22 (7) ◽  
pp. 815-824
Author(s):  
Sedighe Azimi ◽  
Majid Pedram
Keyword(s):  
Date Palm ◽  
Phylogenetic Analyses ◽  
Original Description ◽  
Original Data ◽  
18S Rrna Gene ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
28S Rrna ◽  
Khuzestan Province ◽  
Molecular Phylogenetic

Summary A population of Hemicriconemoides phoenicis was recovered from Khuzestan province, south-western Iran, in association with date palm. The recovered population was characterised by 518-645 μm long females having a 76-82 μm long stylet, rounded to oblong spermatheca filled with sperm, a 28.0-39.8 μm long tail, juveniles common, with 14 longitudinal rows of rounded scales, and males absent. Compared to the original data, no morphological and morphometric differences were observed. In molecular phylogenetic analyses using the D2-D3 expansion segments of the 28S rRNA gene and a near-full-length fragment of the 18S rRNA gene sequences using Bayesian inference (BI) and maximal number of species of the genus, the two newly generated 28S sequences of the Iranian population formed a maximally supported clade with two original sequences of the species; and the 18S sequence formed a maximally supported clade with an unidentified isolate of the genus in the corresponding phylogeny. This is the second report of the species since its original description, Iran representing a new geographical record and supporting the suggestion that date palm could be its preferred host.

Redescription and molecular characterisation of Xiphinema barense Lamberti et al., 1986 (Nematoda: Longidoridae) from wild olive trees in southern Italy

Nematology ◽  
2014 ◽  
Vol 16 (9) ◽  
pp. 1079-1089 ◽  
Author(s):  
Francesca De Luca ◽  
Antonio Archidona-Yuste ◽  
Alberto Troccoli ◽  
Elena Fanelli ◽  
Nicola Vovlas ◽  
...  
Keyword(s):  
Southern Italy ◽  
Phylogenetic Analyses ◽  
Original Description ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Species Differentiation ◽  
Rrna Gene ◽  
28S Rrna ◽  
Wild Olive ◽  
Olive Trees

A population of Xiphinema barense from wild olive trees in Torre Pozzella, Brindisi province, southern Italy, is described using both morphological and molecular studies and compared with the description of the type specimens. The wild olive nematode population agrees very well with all morphometrics provided in the original description. However, detailed observations of the lumen of the tubular portion of the uterus in paratypes and specimens of the new population revealed a clear pseudo-Z-organ with small granules mixed with crystalloid bodies which were previously undetected. Photomicrographs of adult paratypes, which were lacking in the original description, and of specimens of the new population from wild olive trees are provided. The results of the phylogenetic analyses based on the sequences of the D2-D3 expansion regions of the 28S rRNA gene and ITS rRNA genes confirm the species differentiation and indicate the phylogenetic position of X. barense and its relationship with closely related species.

Redescription of Cerebratulus marginatus auct. (Nemertea: Pilidiophora) from Hokkaido, Japan, as a new species

Zootaxa ◽  
2020 ◽  
Vol 4819 (2) ◽  
pp. 295-315
Author(s):  
HIROSHI KAJIHARA
Keyword(s):  
16S Rrna ◽  
Vascular System ◽  
Phylogenetic Analyses ◽  
Far East ◽  
Muscle Layer ◽  
The Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Anterior Portion ◽  
Longitudinal Muscle Layer

The heteronemertean Cerebratulus orochi sp. nov. is described based on material collected intertidally at a muddy beach in Akkeshi, northern Japan. For the last 80 years, the species has been confused with Cerebratulus marginatus Renier, 1804; the latter was originally described from the Adriatic and once believed to occur in many places in the northern hemisphere including Japan. Cerebratulus orochi sp. nov. is morphologically different from all the congeners including C. marginatus by the following combination of characters: several layers of diagonal-muscle meshwork coated with connective tissue, proximo-distally distributed in cross section from the distal portion of the body-wall outer longitudinal muscle layer to the cutis-gland zone throughout the anterior portion of the body from the precerebral to the foregut regions; the cephalic vascular system consisting of lateral and mid-dorsal vessels; and the sub-rhynchocoelic vessel possessing a pair of antero-lateral diverticula before the former forks posteriorly into a pair of lower lateral vessels in the post-cerebral, pre-oral region. Previous records of C. marginatus from Japanese waters are no longer considered to be substantiated. Multi-locus phylogenetic analyses based on the mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI), as well as the nuclear 18S rRNA, 28S rRNA, and histone H3 genes among heteronemerteans comprising the “Cerebratulus clade” indicated that C. orochi sp. nov. was closely related to C. cf. marginatus from the US Pacific coast. A MegaBLAST search at the NCBI website with the 16S rRNA gene sequence from C. orochi sp. nov. followed by a couple of species delimitation analyses suggests that larvae of the species are also distributed in Vostok Bay, Far East Russia.

scholarly journals Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

2008 ◽  
Vol 74 (17) ◽  
pp. 5422-5428 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Noha H. Youssef ◽  
Anne M. Spain ◽  
Cody Sheik ◽  
Fares Z. Najar ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Tall Grass ◽  
Data Set ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Soil Bacterial ◽  
Close Relatives ◽  
Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

Mononchoides macrospiculum n. sp. (Nematoda: Neodiplogastridae) and Teratorhabditis synpapillata Sudhaus, 1985 (Nematoda: Rhabditidae): nematode associates of Rhynchophorus ferrugineus (Oliver) (Coleoptera: Curculionidae) in Italy

Nematology ◽  
2015 ◽  
Vol 17 (8) ◽  
pp. 953-966 ◽  
Author(s):  
Alberto Troccoli ◽  
Monica Oreste ◽  
Eustachio Tarasco ◽  
Elena Fanelli ◽  
Francesca De Luca
Keyword(s):  
Molecular Level ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
28S Rrna ◽  
Italian Population ◽  
Rhynchophorus Ferrugineus ◽  
Red Palm Weevil ◽  
Palm Weevil ◽  
Mitochondrial Cytochrome Oxidase

Several juvenile and adult nematodes were isolated after dissection of pupae and adults of the red palm weevil,Rhynchophorus ferrugineus, recovered from an infestedPhoenix canariensisChabaud exemplar in Bari, Italy. Two species of nematodes were recovered,Teratorhabditis synpapillataandMononchoides macrospiculumn. sp. which is described herein. The mitochondrial cytochrome oxidase I (COI), the ITS-containing region, the 18S rRNA gene (SSU) and the D2-D3 expansion domains of the 28S rRNA gene (LSU) were amplified and sequenced. The new species,M. macrospiculumn. sp., is described at morphological and molecular level. Phylogenetic analyses using SSU and LSU sequences placedM. macrospiculumn. sp. together withM. composticolaandM. striatus. The sequences of the Italian population ofT. synpapillataare identical to those ofT. synpapillatafrom Japan. This is the first report on the association ofM. macrospiculumn. sp. andT. synpapillatawith the red palm weevil in Europe.

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