scholarly journals Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 408
Author(s):  
Phougeishangbam Rolish Singh ◽  
Gerrit Karssen ◽  
Marjolein Couvreur ◽  
Sergei A. Subbotin ◽  
Wim Bert
Keyword(s):  
18S Rrna ◽  
Parasitic Nematode ◽  
Integrative Taxonomy ◽  
Coi Gene ◽  
Integrated Analysis ◽  
Gene Sequences ◽  
Unknown Species ◽  
New Gene ◽  
First Time ◽  
Plant Parasitic

Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.

Redefinition of Cornexcisia Fan & Kano, 2000 (Diptera: Sarcophagidae), with the first description of the female of Sarcophaga kurahashii (Shinonaga & Tumrasvin, 1979)

Zootaxa ◽  
2019 ◽  
Vol 4668 (3) ◽  
pp. 410-420
Author(s):  
CHAO WANG ◽  
YUNYUN GAO ◽  
THOMAS PAPE ◽  
DONG ZHANG
Keyword(s):  
Cytochrome Oxidase ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Gene Sequences ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Senior Synonym ◽  
First Time ◽  
Mitochondrial Cytochrome Oxidase

Sarcophaga Meigen, 1826 is proposed as a senior synonym of Cornexcisia Fan & Kano, 2000, syn. nov. and Fanzideia Xue, Verves & Du, 2011, syn. nov. Cornexcisia Fan & Kano, 2000, stat. rev. is given status as a subgenus and is considered a senior synonym of Fanzideia Xue, Verves & Du, 2011, syn. nov. at the subgeneric level. Cornexcisia is argued to contain S. (Cornexcisia) longicornuta (Fan & Kano, 2000), comb. nov., S. (C.) cygnocerca (Xue, Verves & Du, 2011), comb. nov., S. (C.) kurahashii (Shinonaga & Tumrasvin, 1979), subgen. comb. nov. (from Phallosphaera Rohdendorf) and S. (C.) suthep Pape & Bänziger, 2003, subgen. comb. nov. (from Rosellea Rohdendorf). Sarcophaga (C.) kurahashii is newly recorded from China (Yunnan), the male is redescribed and the female is described for the first time, supported by photographs, illustrations and mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Species of Cornexcisia share an exceptionally long postpedicel in the female and the following apomorphic distiphallic appendages in the male: juxta ventro-proximally with an apically divided arm with cuticular pile, and lateral styli bifurcated from the base with each branch elongate, gently curved and slightly expanded apically. A key to the species of Cornexcisia is provided. 

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 Karyotype and COI gene sequence of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the Gydan Peninsula, Russia

2021 ◽  
Vol 15 (4) ◽  
pp. 447-458
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin ◽  
Sergey V. Artemenko
Keyword(s):  
Phylogenetic Tree ◽  
Gene Sequence ◽  
Genetic Distances ◽  
Coi Gene ◽  
Gene Sequences ◽  
South Caucasus ◽  
Homozygous State ◽  
Banding Sequence ◽  
First Time ◽  
Georgian Population

The karyotype features and gene COI sequence of Chironomus heteropilicornis Wülker, 1996 from the Gydan Peninsula are presented for the first time. Nine banding sequences were determined, eight of them hpiA2, hpiB1, hpiC1, hpiC2, hpiD1, hpiE1, hpiF3 and hpiG1 were previously known from European, Georgian (South Caucasus) and Siberian populations. One new banding sequence for Ch. heteropilicornis, hpiB2, was found. The hpiA2 banding sequence was found in all individuals, and this is its second finding after the Georgian population (Karmokov 2019). The hpiF3 banding sequence was found only in the homozygous state. Additional B-chromosomes are absent. The genetic distances (K2P) between Ch. heteropilicornis COI gene sequence from Gydan Peninsula and Norway are 1.1­–1.3%, and Georgia – 1.8%, much lower than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. The phylogenetic tree for COI gene sequences estimated by Bayesian inference showed geographically determined clusters of Norway and Gydan and a separate lineage of the Georgian population of Ch. heteropilicornis. The analysis of karyotype and COI gene sequences shows that the population of Ch. heteropilicornis from the Gydan Peninsula has an intermediate position within the Ch. pilicornis group between Georgian, Yakutian and Norwegian populations. The position of Ch. pilicornis Fabricius, 1787 from Canada and Greenland on the phylogenetic tree is discussed.

The pitfalls of molecular species identification: a case study within the genus Pratylenchus (Nematoda: Pratylenchidae)

Nematology ◽  
2017 ◽  
Vol 19 (10) ◽  
pp. 1179-1199 ◽  
Author(s):  
Toon Janssen ◽  
Gerrit Karssen ◽  
Marjolein Couvreur ◽  
Lieven Waeyenberge ◽  
Wim Bert
Keyword(s):  
Molecular Species ◽  
Dna Sequences ◽  
Parasitic Nematode ◽  
Crucial Importance ◽  
Free Living ◽  
Molecular Analyses ◽  
Molecular Species Identification ◽  
First Time ◽  
Plant Parasitic

Comprehensive morphological and molecular analyses revealed that published ITS sequences of the economically important plant-parasitic nematodePratylenchus goodeyiare actually sequences from distantly free-living bacterivorous ‘cephalobids’. We demonstrated that this incorrect labelling resulted in a cascade of erroneous interpretations, as shown by the reports of ‘P. goodeyi’ on banana in China and on cotton in India. This clearly illustrates the risk of mislabelled sequences in public databases. Other mislabelledPratylenchuscases are discussed to illustrate that this is not an isolated case. Herein,P. lentisn. syn. is considered a junior synonym ofP. pratensiswhileP. flakkensiswas for the first time linked to DNA sequences using topotype material. As taxonomic expertise is decreasing and sequence-based identification is growing rapidly, the highlighted problem may yet increase and a strong link between morphology and DNA sequences will be of crucial importance in order to prevent, or at least minimise, sequence-based misidentifications.

scholarly journals Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e60891 ◽  
Author(s):  
Seloame T. Nyaku ◽  
Venkateswara R. Sripathi ◽  
Ramesh V. Kantety ◽  
Yong Q. Gu ◽  
Kathy Lawrence ◽  
...  
Keyword(s):  
18S Rrna ◽  
Parasitic Nematode ◽  
18S Rrna Gene ◽  
Plant Parasitic Nematode ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Rotylenchulus Reniformis ◽  
Plant Parasitic

scholarly journals Phylogenetic Analysis of Indian Freshwater Pond Mussels Lamellidens corrianus and L. phenchooganjensis (Bivalvia: Unionidae) from the Upper Brahmaputra Basin of Assam, India

2021 ◽  
Vol 18 (1) ◽  
pp. 197-206
Author(s):  
Jyotish Sonowal ◽  
Pankaj Chetia ◽  
Devid Kardong
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Gene Sequence ◽  
18S Rrna Gene ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequences ◽  
Freshwater Molluscs ◽  
First Time

To update the present knowledge of freshwater molluscs, a phylogenetic analysis of two species of Indian pond mussels was carried out using amplified sequence of 18S rRNA gene. From the phylogenetic study of 18S rRNA gene sequencing, it was found that the Lamellidenscorrianus and L. phenchooganjensis are phylogenetically closely related to 18S rRNA gene sequences of other freshwater bivalve mussels belonging to the family Unionidae of order Unionida. Like other members of the Unionidae family, the two Lamellidensspp. showed monophyletic evolutionary lineage and shared a common ancestor. The result obtained from the phylogenetic analysis of Lamellidensspp. was significant as the 18S rRNA gene sequence of L. phenchooganjensis was submitted for the first time in the global nucleotide database (Genbank, NCBI). Similarly, the 18S rRNA gene sequence of L. corrianuswas also submitted to the database for the first time from this region having unique ecological niche. Therefore, the present study on phylogenetic analysis is a contribution to the global database of 18S rRNA gene sequences of freshwater mollusc, particularly from this part of the region.

Morphological characterisation and molecular phylogeny of several species of Criconematina (Nematoda: Tylenchida) associated with turfgrass in Korea, as inferred from ribosomal and mitochondrial DNA

Nematology ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. 939-956 ◽  
Author(s):  
Abraham Okki Mwamula ◽  
Md. Faisal Kabir ◽  
Gayeong Lee ◽  
In Ho Choi ◽  
Young Ho Kim ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Integrative Taxonomy ◽  
Coi Gene ◽  
Sequence Information ◽  
28S Rrna ◽  
Operational Taxonomic Units ◽  
Gene Sequence Analysis ◽  
Molecular Phylogenetic ◽  
The Usa ◽  
First Time

Summary Six species belonging to the Criconematina, including a morphologically cryptic population within the Mesocriconema curvatum-group, are characterised based on integrative taxonomy based on morphological and molecular phylogenetic inferences from analyses of the 28S-rRNA, ITS-rRNA and COI gene sequences. Mesocriconema sp. 1 is morphologically similar to M. nebraskense and M. curvatum, differing from M. curvatum by the occasional presence of 1-2 anastomoses and a relatively higher R value, and from M. nebraskense by only a narrowed first lip annulus. However, based on COI gene sequence analysis, significant differences among the three species are evident. The sequence information in the COI gene among Mesocriconema spp. continues to reveal the existence of cryptic species within well-established species designations, and the concept of Molecular Operational Taxonomic Units might be helpful in grouping the different lineages according to sequence identities. Mesocriconema nebraskense is detailed herein for the first time outside the USA. DNA sequences of Hemicycliophora labiata were similar to those in GenBank while the existence in Korea of M. curvatum, Hemicriconemoides brachyurus and Paratylenchus nanus is molecularly confirmed.

scholarly journals Transcriptional signatures of invasiveness inMeloidogyne incognitapopulations from sub-Saharan Africa

2019 ◽  
Author(s):  
Deborah Cox ◽  
Brian Reilly ◽  
Neil D. Warnock ◽  
Steven Dyer ◽  
Matthew Sturrock ◽  
...  
Keyword(s):  
Parasitic Nematode ◽  
Host Finding ◽  
Sub Saharan Africa ◽  
Substantial Variation ◽  
Cell Wall Degrading Enzymes ◽  
Protein Coding ◽  
Non Coding Rnas ◽  
Sub Saharan ◽  
First Time ◽  
Plant Parasitic

AbstractMeloidogyne incognitais an economically important plant parasitic nematode. Here we demonstrate substantial variation in the invasiveness of fourM. incognitapopulations relative to tomato. Infective (J2) stage transcriptomes reveal significant variation in the expression of protein-coding and non-coding RNAs between populations. We identify 33 gene expression markers (GEMs) that correlate with invasiveness, and which map to genes with predicted roles in host-finding and invasion, including neuropeptides, ion channels, GPCRs, cell wall-degrading enzymes and microRNAs. These data demonstrate a surprising diversity in microRNA complements between populations, and identify GEMs for invasiveness ofM. incognitafor the first time.

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