Length variation and repetitive sequences of Internal Transcribed Spacer of ribosomal RNA gene, diagnostics and relationships of populations of potato rot nematode, Ditylenchus destructor Thorne, 1945 (Tylenchida: Anguinidae)

Nematology ◽  
2011 ◽  
Vol 13 (7) ◽  
pp. 773-785 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Abbas Mohammad Deimi ◽  
Jingwu Zheng ◽  
Vladimir N. Chizhov
Keyword(s):  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Repetitive Elements ◽  
Rrna Gene ◽  
Length Variation ◽  
28S Rrna ◽  
Gene Sequences ◽  
Its Rrna Gene ◽  
Its Rrna ◽  
Ditylenchus Destructor

Abstract Seventy-eight ITS rRNA gene sequences obtained from the potato rot nematode, Ditylenchus destructor, collected across the world from different hosts were compared and analysed. The ITS rRNA gene sequences showed significant length variation between populations. The differences in this rRNA fragment length were due to the presence of repetitive elements in the ITS1, which were characterised by relatively higher rates of substitution changes. Reconstruction of secondary structure for the ITS1 revealed that these minisatellites formed a stem structure. Phylogenetic analyses of ITS rRNA and D2-D3 expansion segments of 28S rRNA gene sequences showed that all studied populations clustered in two major clades: a group of populations having the ITS sequences with the repetitive elements and a group of populations without the repetitive elements in the ITS. We propose to distinguish seven ITS rRNA haplotypes within potato rot nematode populations. PCR-ITS-RFLP diagnostic profiles are presented for these ITS haplotypes and usefulness of recently developed PCR methods with species-specific primers for D. destructor are analysed and discussed.

DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the Avenae group from the genus Heterodera (Tylenchida: Heteroderidae)

Nematology ◽  
2018 ◽  
Vol 20 (7) ◽  
pp. 671-702 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Fateh Toumi ◽  
Ibrahim Halil Elekçioğlu ◽  
Lieven Waeyenberge ◽  
Zahra Tanha Maafi
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Nematode Species ◽  
Cyst Nematode ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Cyst Nematodes ◽  
Long Distance ◽  
Its Rrna Gene ◽  
Its Rrna

Summary Among the recognised species groups of Heterodera, the Avenae group is one of the largest with a total of 12 species. Ten of them, H. arenaria, H. aucklandica, H. australis, H. avenae, H. filipjevi, H. mani, H. pratensis, H. riparia, H. sturhani and H. ustinovi, are morphologically closely related and represent the H. avenae species complex, and the other two, H. hordecalis and H. latipons, are morphologically more distinct from this complex. In this study we provide comprehensive phylogenetic analyses of several hundred COI and ITS rRNA gene sequences from the Avenae group using Bayesian inference, maximum likelihood and statistical parsimony. Some 220 COI and 11 ITS rRNA new gene sequences from 147 nematode populations collected in 26 countries were obtained in this study. Our study showed that the COI gene is a powerful DNA barcoding marker for identification of populations and species from the Avenae group. A putatively new cyst nematode species related to H. latipons was revealed from the analysis of COI and ITS rRNA gene datasets. COI gene sequences allow distinguishing H. arenaria, H. australis and H. sturhani from each other and other species. Problems of species delimiting of these species are discussed. The results of the analysis showed that COI haplotypes corresponded to certain pathotypes of the cereal cyst nematodes. It is recommended that information on COI haplotypes of studied populations be included in research with these nematodes. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that several species of the Avenae group primarily originated and diversified in the Irano-Anatolian hotspot during the Pleistocene and Holocene periods and then dispersed from this region across the world. Different geographic barriers, centres and times of origin might explain current known distribution patterns for species of the Avenae group. Possible pathways, including a long distance trans-Atlantic dispersal, and secondary centres of diversification are proposed and discussed.

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 studies on Heterodera sacchari, H. goldeni and H. leuceilyma (Nematoda: Heteroderidae)

Nematology ◽  
2007 ◽  
Vol 9 (4) ◽  
pp. 483-497 ◽  
Author(s):  
Zahra Tanha Maafi ◽  
Dieter Sturhan ◽  
Zafar Handoo ◽  
Mishael Mor ◽  
Maurice Moens ◽  
...  
Keyword(s):  
Species Complex ◽  
Morphological Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
African Countries ◽  
Time Reproduction ◽  
Its Rrna Gene ◽  
Its Rrna ◽  
First Time ◽  
Sugarcane Ratoon

AbstractHeterodera sacchari, H. leuceilyma and H. goldeni are closely related members of the H. sacchari species complex, which is mainly characterised and distinguished from all other described Heterodera species by the presence of finger-like projections of the strongly developed underbridge in the vulval cone of the cysts. Males are rare in all three species and are described here in H. goldeni for the first time. Reproduction appears to be parthenogenetic. There are only minor morphological distinctions between the three species, particularly after our present studies have emended their original descriptions from various populations. Heterodera sacchari and H. goldeni showed differences in the ITS-rRNA gene sequences. Heterodera sacchari was described and reliably identified from many tropical African countries, H. leuceilyma is known only from Florida, USA, and H. goldeni has been identified in Egypt, Israel and Iran. All three species have grasses and other Poaceae as hosts, H. sacchari commonly attacking rice and sugarcane, and H. goldeni reproducing successfully on sugarcane ratoon seedlings. Morphological data emending the descriptions of H. sacchari, H. goldeni and H. leuceilyma from various populations are presented and discussed along with their host and distribution. Molecular characterisation of H. sacchari and H. goldeni is provided. An analysis of phylogenetic relationships within species of the sacchari-group using ITS-rRNA gene sequences is also presented.

Molecular phylogeny of several species of Hoplolaimina (Nematoda: Tylenchida) associated with turfgrass in Korea, with comments on their morphology

Nematology ◽  
2020 ◽  
pp. 1-18
Author(s):  
Abraham Okki Mwamula ◽  
Gayeong Lee ◽  
Yeong Ho Kim ◽  
Young Ho Kim ◽  
Kwang-Soo Lee ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Integrative Taxonomy ◽  
Rrna Genes ◽  
28S Rrna ◽  
Gene Sequences ◽  
Meloidogyne Graminicola ◽  
Molecular Phylogenetic ◽  
Its Rrna ◽  
First Time ◽  
Pratylenchus Zeae

Summary Seven species belonging to Suborder Hoplolaimina are characterised using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 28S-rRNA, ITS-rRNA and COI gene sequences. It is evident that, as more populations of Pratylenchus zeae are continuously characterised, the species continues to display an ever-increasing intraspecific genetic variation within the 28S-rRNA and ITS-rRNA genes. However, the COI gene sequences exhibit minimum intraspecific variation and thus might be the most powerful DNA barcoding marker for the precise identification of P. zeae and should therefore be recommended as a complementary technique in the identification process of the species. Pratylenchus zeae, Meloidogyne graminicola and Heterodera pratensis are characterised herein for the first time in Korea, while the presence in Korea of P. penetrans, P. scribneri, H. avenae, and M. marylandi, is molecularly confirmed.

Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 323-358 ◽  
Author(s):  
Esther Van den Berg ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
...  
Keyword(s):  
South Africa ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Wide Range ◽  
Its Rrna Gene ◽  
Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

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.

Characterisation of populations of Heterodera trifolii Goffart, 1932 (Nematoda: Heteroderidae) in Japan and their phylogenetic relationships with closely related species

Nematology ◽  
2017 ◽  
Vol 19 (5) ◽  
pp. 543-558
Author(s):  
Shigeyuki Sekimoto ◽  
Taketo Uehara ◽  
Takayuki Mizukubo
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
Closely Related Species ◽  
28S Rrna Gene ◽  
Intraspecific Variations ◽  
Low Levels

The Japanese populations of the clover cyst nematode,Heterodera trifolii, were characterised morphologically, morphometrically and molecularly. The morphology and morphometrics of six Japanese populations ofH. trifoliiwere in congruence with those of previous descriptions of this species from Germany, Italy, Japan, New Zealand, Russia, The Netherlands, UK and USA. The results of the phylogenetic analyses of the D2-D3 expansion segments of 28S rRNA gene and theCOImtDNA gene sequences discriminatedH. trifoliifrom most of the other closely related species of theSchachtiigroup. The intraspecific sequence differences in theSchachtiigroup were much higher inCOIthan in D2-D3. TheH. trifoliipopulations displayed very low levels of intraspecific variations (up to 0.3%) in theCOImtDNA gene sequences. The phylogenetic relationships ofH. trifoliiwith otherHeteroderaspecies, as inferred from the analyses of the ITS rRNA gene, D2-D3 of 28S rRNA gene andCOImtDNA gene sequences, were determined.

DNA barcoding, phylogeny and phylogeography of the cyst nematode species from the genus Globodera (Tylenchida: Heteroderidae)

Nematology ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. 269-297 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Javier Franco ◽  
Rinus Knoetze ◽  
Tatiana V. Roubtsova ◽  
Richard M. Bostock ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Economic Losses ◽  
Rrna Gene ◽  
Undescribed Species ◽  
Gene Sequences ◽  
Cyst Nematodes ◽  
Isolated Populations ◽  
The World ◽  
Its Rrna

Summary Globodera presently contains 13 valid and three as yet undescribed species. Three species, G. rostochiensis, G. pallida and G. ellingtonae, the potato cyst nematodes (PCN), cause significant economic losses on potatoes around the world. In our study we provide comprehensive phylogenetic analyses of 455 ITS rRNA, 219 COI and 164 cytb gene sequences of 11 valid and two undescribed species of Globodera using Bayesian inference, maximum likelihood and statistical parsimony. New 205 COI, 116 cytb and 21 ITS rRNA gene sequences were obtained from 148 populations of these species collected from 23 countries. The phylogenetic analysis revealed that Globodera displayed two main clades in the trees: i) Globodera from South and North America parasitising plants from Solanaceae; and ii) Globodera from Africa, Europe, Asia and New Zealand parasitising plants from Asteraceae and other families. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it is hypothesised that Globodera species originated and diversified from several centres of speciation located in mountain regions and then dispersed across the world from these regions during the Pleistocene. High genetic diversity of Bolivian populations of G. rostochiensis was observed for both mtDNA genes. Analysis of phylogenetic relationships of G. pallida and G. rostochiensis populations revealed incongruence in topology between networks inferred from mtDNA genes, which might be an indication of possible recombination and selective introgression events through gene flow between previously isolated populations. This puts some limitations on the use of the mtDNA marker as universal DNA barcoding identifier for PCN. Globodera bravoae syn. n. is proposed as a junior synonym of G. mexicana.

Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).

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