Morphological and molecular characterisation of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from India

Nematology ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 439-452 ◽  
Author(s):  
Suman ◽  
Aashaq Hussain Bhat ◽  
Aasha ◽  
Ashok Kumar Chaubey ◽  
Joaquín Abolafia
Keyword(s):  
Phylogenetic Trees ◽  
Agricultural Soils ◽  
Phylogenetic Analyses ◽  
Uttar Pradesh ◽  
Sister Group ◽  
Molecular Characterisation ◽  
Soil Baiting ◽  
Its Rrna ◽  
First Time ◽  
Rrna Sequences

Summary A redescription of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from agricultural soils in Uttarakhand and Uttar Pradesh, India, is provided. Specimens were extracted from soil using the Galleria soil baiting technique, with two strains of nematodes named JP1 and JP2 being obtained. Morphological and morphometric studies on the species agree well with previous records. Molecular analyses are provided using 18S, 28S and ITS rRNA sequences, the ITS sequences being obtained for the first time in this species. These analyses show that the material examined agrees well with previously studied populations. Phylogenetic analyses showed Distolabrellus to be the sister group of Crustorhabditis and Teratorhabditis, all having the male spicules fused for more than 50% of their length. Illustrations and phylogenetic trees based on 18S, 28S and ITS rRNA sequences are provided.

Phylogenetic relationships of Cacopaurus pestis Thorne, 1943 within representatives of the Tylenchulidae Skarbilovich, 1947 as inferred from ITS and D2-D3 expansion segments of 28S-rRNA sequences

Nematology ◽  
2019 ◽  
Vol 21 (9) ◽  
pp. 971-994 ◽  
Author(s):  
Abas Mokaram Hesar ◽  
Akbar Karegar ◽  
Reza Ghaderi
Keyword(s):  
Plant Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Stylet Length ◽  
Ectoparasitic Nematodes ◽  
North Western ◽  
Rrna Sequences

Summary The Persian sessile nematode (Cacopaurus pestis) and pin nematodes (Paratylenchus spp.) are sedentary ectoparasitic nematodes associated with many plant species worldwide. In this study, we provide morphological and molecular characterisation of seven populations of C. pestis and eight species of Paratylenchus recovered from north-western Iran. A total of 26 new sequences of D2-D3 expansion segments of 28S rRNA and ITS rRNA were obtained and used to reconstruct phylogenetic trees. Results of phylogenetic analyses revealed that the subfamilies of Tylenchulidae form well-separated clades, but that the genera Cacopaurus and Paratylenchus (= Gracilacus) in the subfamily Paratylenchinae are clustered in one clade. It appears that the previously used character of “stylet length greater than 40 μm” is not homologous and evolved more than once within the Paratylenchinae.

scholarly journals Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Jian-Qiu Li ◽  
Li Li ◽  
Bao-Quan Fu ◽  
Hong-Bin Yan ◽  
Wan-Zhong Jia
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Sister Group ◽  
Trna Genes ◽  
Mammal Species ◽  
Qinghai Province ◽  
Loop Region ◽  
Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

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.

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

scholarly journals Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽  
2021 ◽  
Vol 1070 ◽  
pp. 13-30
Author(s):  
Wanqing Zhao ◽  
Dajun Liu ◽  
Qian Jia ◽  
Xin Wu ◽  
Hufang Zhang
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Purifying Selection ◽  
Sister Group ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

scholarly journals Evolutionary Relationships among Primary Endosymbionts of the Mealybug Subfamily Phenacoccinae (Hemiptera: Coccoidea: Pseudococcidae)

2010 ◽  
Vol 76 (22) ◽  
pp. 7521-7525 ◽  
Author(s):  
Matthew E. Gruwell ◽  
Nate B. Hardy ◽  
Penny J. Gullan ◽  
Katharina Dittmar
Keyword(s):  
16S Rrna ◽  
Nucleotide Substitution ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Buchnera Aphidicola ◽  
Free Living ◽  
Bacterial Endosymbionts ◽  
Rrna Sequences ◽  
Living Bacteria ◽  
16S Rrna Sequences

ABSTRACT Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria (“Candidatus Tremblaya princeps”) containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to “Candidatus Tremblaya princeps.” Names are proposed for two strongly supported lineages: “Candidatus Brownia rhizoecola” for P-endosymbionts of Rhizoecini and “Candidatus Tremblaya phenacola” for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids (“Candidatus Buchnera aphidicola”), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.

scholarly journals Complete mitogenomes of Anopheles peditaeniatus and Anopheles nitidus and phylogenetic relationships within the genus Anopheles inferred from mitogenomes

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jing Guo ◽  
Zhen-Tian Yan ◽  
Wen-Bo Fu ◽  
Huan Yuan ◽  
Xu-Dong Li ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Repeat Unit ◽  
Taxonomic Revision ◽  
Sister Group ◽  
The Other ◽  
Genome Variations ◽  
Medical Importance ◽  
First Time

Abstract Background Despite the medical importance of mosquitoes of the genus Anopheles in the transmission of malaria and other human diseases, its phylogenetic relationships are not settled, and the characteristics of mitochondrial genome (mitogenome) are not thoroughly understood. Methods The present study sequenced and analyzed the complete mitogenomes of An. peditaeniatus and An. nitidus, investigated genome characteristics, and inferred the phylogenetic relationships of 76 Anopheles spp. Results The complete mitogenomes of An. peditaeniatus and An. nitidus are 15,416 and 15,418 bp long, respectively, and both include 13 PCGs, 22 tRNAs, two tRNAs and one control region (CR). Mitogenomes of Anopheles spp. are similar to those of other insects in general characteristics; however, the trnR and trnA have been reversed to “trnR-trnA,” as has been reported in other mosquito genera. Genome variations mainly occur in CR length (493–886 bp) with six repeat unit types identified for the first time that demonstrate an evolutionary signal. The subgenera Lophopodomyia, Stethomyia, Kerteszia, Nyssorhynchus, Anopheles and Cellia are inferred to be monophyletic, and the phylogenetic analyses support a new phylogenetic relationship among the six subgenera investigated, in that subgenus Lophopodomyia is the sister to all other five subgenera, and the remaining five subgenera are divided into two clades, one of which is a sister-taxon subgenera Stethomyia + Kerteszia, and the other consists of subgenus Nyssorhynchus as the sister to a sister-group subgenera Anopheles + Cellia. Four series (Neomyzomyia, Pyretophorus, Neocellia and Myzomyia) of the subgenus Cellia, and two series (Arribalzagia and Myzorhynchus) of the subgenus Anopheles were found to be monophyletic, whereas three sections (Myzorhynchella, Argyritarsis and Albimanus) and their subdivisions of the subgenus Nyssorhynchus were polyphyletic or paraphyletic. Conclusions The study comprehensively uncovered the characteristics of mitogenome and the phylogenetics based on mitogenomes in the genus Anopheles, and provided information for further study on the mitogenomes, phylogenetics and taxonomic revision of the genus. Graphical abstract

Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes

Zootaxa ◽  
2009 ◽  
Vol 2080 (1) ◽  
pp. 55-68 ◽  
Author(s):  
HUI LIU ◽  
PING ZHAO ◽  
SHUJUAN LI ◽  
WANZHI CAI
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Nuclear Gene ◽  
Taxonomic Status ◽  
Sister Group ◽  
Molecular Data ◽  
28S Rrna ◽  
Minimum Evolution ◽  
Morphological Studies

In this study, we used three mitochondrial genes (cyt b, COI, and 16S rRNA) and one nuclear gene (28S rRNA) to evaluate the current taxonomic status of the genus Velinoides erected by Matsumura. Phylogenetic analyses of genes using maximum parsimony, maximum likelihood, and minimum evolution resulted in different phylogenetic trees. However, the combined dataset analysis revealed better phylogenetic relationships. The constructed phylogenies appeared to be largely congruent with morphological studies. Results based on the molecular data strongly supported that the C. dilatatus, the type species of Velinoides, was the sister group to all other species of the genus Coranus Curtis. Incorporation with the morphological and cytogenetic characteristics, we proposed that Velinoides is of subgeneric status, the genus Coranus Curtis should be divided into two subgenera, Velinoides Matsumura and Coranus Curtis. Our phylogenetic results suggested that the 28S rDNA gene segment alone might not be an optimal molecular marker for the phylogeny of the genus Coranus Curtis.

Hirschmanniella kwazuna sp. n. from South Africa with notes on a new record of H. spinicaudata (Schuurmans Stekhoven, 1944) Luc & Goodey, 1964 (Nematoda: Pratylenchidae) and on the molecular phylogeny of Hirschmanniella Luc & Goodey, 1964

Nematology ◽  
2009 ◽  
Vol 11 (4) ◽  
pp. 523-540 ◽  
Author(s):  
Esther Van den Berg ◽  
Sergei A. Subbotin ◽  
Zafar A. Handoo ◽  
Louwrens R. Tiedt
Keyword(s):  
South Africa ◽  
Phylogenetic Analyses ◽  
Body Cavity ◽  
Rrna Genes ◽  
Entire Body ◽  
Lateral Field ◽  
Molecular Sequence ◽  
Its Rrna ◽  
Tail Tip ◽  
First Time

Abstract A new species of the genus Hirschmanniella, H. kwazuna sp. n., is described from unidentified grass growing in undisturbed veldt from South Africa. Hirschmanniella kwazuna sp. n. is characterised by having a very irregular heat-relaxed body posture, body 1522-2049 μm long, lip region low and rounded with four or five lip annuli, stylet 18-22.5 μm long, lateral field areolated along entire body, spermatheca filled with sperm, tail with 62-81 ventral annuli narrowing to a tip bearing a ventral mucro, angular crystal-like inclusions within body cavity in most of the specimens and phasmid situated 12-24 annuli or 15-26 μm anterior to tail tip. Males, like females, have crystal-like inclusions with the tail curved strongly dorsad in most specimens. Juveniles are similar to females. Molecular sequence analysis using the D2-D3 expansion segments of 28S, partial 18S and ITS rRNA sequences distinguished H. kwazuna sp. n. from H. loofi and other species of the genus. Hirschmanniella spinicaudata is reported from South Africa for the first time and described. Phylogenetic analyses based on analysis of the D2-D3, 18S and ITS rRNA genes are given for eight, ten and five valid and unidentified Hirschmanniella species, respectively.

scholarly journals Description and molecular phylogeny of Tethya leysae sp. nov. (Porifera, Demospongiae, Hadromerida) from the Canadian Northeast Pacific with remarks on the use of microtomography in sponge taxonomy

Zootaxa ◽  
2010 ◽  
Vol 2422 (1) ◽  
pp. 1 ◽  
Author(s):  
ISABEL HEIM ◽  
MICHAEL NICKEL
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Dense Layer ◽  
Morphometric Measurements ◽  
Northeast Pacific ◽  
Species Cluster ◽  
Morphological Differences ◽  
First Time ◽  
A New Species

The sponge Tethya leysae sp. nov. (Porifera, Demospongiae, Hadromerida, Tethyidae) is a new species from the Canadian Northeast Pacific. Its type locality is the infralittoral around Ohiat Islet, Barkely Sound, Vancouver Island in Canada. Tethya leysae sp. nov. is a medium-sized spherical sponge with a verrucose surface, orange-yellow to light red alive and white with a greyish core in ethanol. The highly variable oxyspherasters (25-115 µm in size, R/C 0.34-0.69) are densely scattered almost throughout the entire cortex. The micrasters comprise acanthoxyspherasters, acanthostrongylasters, acanthotylasters and small oxyspherasters, which are present at low densities throughout the sponge and form a dense layer associated with the exopinacoderm. The megascleres and the auxiliary megascleres comprise oxeas and strongyloxeas. The new species is clearly distinguishable from the closely related T. californiana by the absence of spherules among the micrasters, the lack of an alveolar cortex and the extremely high density of megasters in the cortex. In addition, the R/C values of the megasters differ between the two species and the oxyspherasters of T. leysae sp. nov. rarely display bent rays. The morphological differences between the species are confirmed by nucleotide and amino acid substitutions within the cytochrome oxidase subunit I (COI) mtDNA gene. Phylogenetic analyses group T. leysae sp. nov. with T. californiana, T. actinia and T. minuta, which together form a sister group to a MediterraneanNorth Atlantic species cluster. Morphological analyses of the skeleton included x-ray microtomography (µCT) and virtual 3D reconstruction, which was used for the first time in conjunction with the description of a new sponge species. Microtomography permitted the visualization and analysis of spicules within the skeletal context or isolated in silico. The method represents a valuable extension to the sponge taxonomist’s toolbox since it allows morphometric measurements in 3D. µCT will thus supplement classical morphological methods such as light and scanning electron microscopy.

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