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 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.

Male identification, generic classification and sexual dimorphism of Micronychus pardus (Kazantsev, 2018) comb. nov. (Coleoptera: Lycidae: Calochrominae)

Zootaxa ◽  
2019 ◽  
Vol 4657 (1) ◽  
pp. 177-182 ◽  
Author(s):  
MICHAL MOTYKA
Keyword(s):  
Mitochondrial Dna ◽  
Sexual Dimorphism ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Large Specimen ◽  
Molecular Analyses ◽  
Almost All ◽  
First Time

Almost all net-winged beetles are members of Müllerian complexes and their similarity due to phenotypic coevolution sometimes complicates species identification and generic placement. Therefore, large specimen series, detailed exhaustive examination of morphological characters and molecular data are needed to clarify the taxonomic placement. Using mitochondrial DNA sequences, I investigated the sexual dimorphism and generic placement of the recently described species Calochromus pardus Kazantsev, 2018. I found that the species does not belong in Calochromus Guérin-Méneville, 1833 and all morphological characters and molecular analyses point to its placement in Micronychus Motschulsky, 1861. Therefore, Micronychus pardus (Kazantsev, 2018), comb. nov. is proposed. Additionally, the male is described here for the first time showing the sexual dimorphism in the species. Unlike the females, the males do not superficially resemble members of Xylobanus Waterhouse, 1879 with bright coloured elytral costae and black background, but mimics the sympatrically occurring yellow and black lycids in the genus Cautires Waterhouse, 1879. 

scholarly journals Molecular Characterization and Phylogenetic Relationships of Plant-Parasitic Nematodes Associated with Turfgrasses in North Carolina and South Carolina, United States

Plant Disease ◽  
2015 ◽  
Vol 99 (7) ◽  
pp. 982-993 ◽  
Author(s):  
Yongsan Zeng ◽  
Weimin Ye ◽  
James Kerns ◽  
Lane Tredway ◽  
Samuel Martin ◽  
...  
Keyword(s):  
North Carolina ◽  
South Carolina ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Parasitic Nematode ◽  
Nematode Species ◽  
Plant Parasitic Nematode ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Plant Parasitic

The near-full-length 18S ribosomal DNA (rDNA) gene and internal transcribed spacer 1 region were amplified and sequenced from 52 nematode populations belonging to 28 representative species in 13 families recovered from turfgrasses in North Carolina (38 populations) and South Carolina (14 populations). This study also included 13 nematode populations from eight other plant hosts from North Carolina for comparison. Nematodes were molecularly characterized and the phylogenetic relationships were explored based on 18S rDNA sequences. Phylogenetic analysis using Bayesian inference was performed using five groups of the plant-parasitic nematode populations Tylenchids, Criconematids, Longidorids, Xiphinematids, and Trichodorids. The 65 nematode populations were clustered correspondingly within appropriate positions of 13 families, including Belonolaimidae, Caloosiidae, Criconematidae, Dolichodoridae, Hemicycliophoridae, Hoplolaimidae, Heteroderidae, Longidoridae, Meloidogynidae, Paratylenchidae, Pratylenchidae, Telotylenchidae, and Trichodoridae. This study confirms previous morphological-based identification of the plant-parasitic nematode species found in turfgrasses and provides a framework for future studies of plant-parasitic nematodes associated with turfgrasses based upon DNA sequences and phylogenetic relationships.

scholarly journals DIVERSITY AND ABUNDANCE OF NEMATODES IN GUAVA (Psidium guajava L.) CULTIVATION IN LAMPUNG

2021 ◽  
Vol 21 (2) ◽  
pp. 134-143
Author(s):  
Nabilah Nabilah ◽  
I Gede Swibawa ◽  
Radix Suharjo ◽  
Yuyun Fitriana
Keyword(s):  
Parasitic Nematode ◽  
Psidium Guajava ◽  
Laboratory Analysis ◽  
Parasitic Nematodes ◽  
Science Laboratory ◽  
Plant Parasitic Nematodes ◽  
Free Living ◽  
Plant Pest ◽  
Free Living Nematode ◽  
Plant Parasitic

Diversity and abundance of nematodes in guava (Psidium guajava L.) cultivation in Lampung. Crystal guava agroecosystem is inhabited by many species of plant parasitic nematodes. However, information regarding this topic was still limited. This study aimed to understand the species dominancy of nematodes in crystal guava cultivation in Lampung. Sampling was carried out in three locations of guava crystal plantations: Lampung Timur, Lampung Tengah, and Tanggamus. The laboratory analysis was done at the Plant Pest Science Laboratory and Agricultural Biotechnology Laboratory, Universitas Lampung. The study was conducted in December 2019 – July 2020. Nematodes were identified to the level of the genus. The Prominance value (PV) was used to assess the nematodes genus dominancy. The results showed that the nematodes inhabiting the crystal guava agro-ecosystem in Lampung was both plant parasitic and free-living nematodes. The plant parasitic nematodes were identified as Meloidogyne, Aphelenchus, Hemicriconemoides, Tylenchus, Aphelenchoides, and Xiphinema, while free-living nematodes was Rhabditis, Dorylaimine, Dorylaimus, and Mononchus. The dominant plant parasitic nematode was Meloidogyne and the dominant free-living nematode was Rhabditis. The abundance of Meloidogyne /300 mL of soil was 351.47 individuals in Lampung Timur, 124.27 individuals in Lampung Tengah, and 82.18 individuals in Tanggamus. The dominant free-living nematode in the three locations was Rhabditis.

New enchytraeid species from Mount Hallasan (Jeju Island, Korea) (Enchytraeidae, Oligochaeta)

Zootaxa ◽  
2018 ◽  
Vol 4496 (1) ◽  
pp. 337 ◽  
Author(s):  
KLÁRA DÓZSA-FARKAS ◽  
TAMÁS FELFÖLDI ◽  
HAJNALKA NAGY ◽  
YONG HONG
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Jeju Island ◽  
Molecular Analyses ◽  
As Species ◽  
First Time

The enchytraeid fauna of Mt. Hallasan (Jeju Island, Korea) was studied in 2016, and 21 enchytraeid species were recorded and identified in total. A combination of morphological and molecular analyses (based on CO1, ITS and H3 sequences) was applied. Here we give descriptions of eight new species of Enchytraeidae (Clitellata): Achaeta koreana sp. n., Achaeta macroampullacea sp. n., Bryodrilus hallasanensis sp. n., Chamaedrilus baekrokdamensis sp. n., Enchytronia seongpanakiensis sp. n., Mesenchytraeus jungsaihoi sp. n., Xetadrilus jejuensis sp. n. and Xetadrilus aphanoides sp. n. Additionally, two species were found to be new for the Korean fauna in Mt. Hallasan: Fridericia cf. paroniana Issel, 1904 and F. perrieri (Vejdovský, 1878); three potentially new Fridericia species require further studies. Furthermore, two terrestrial polychaetes, Hrabeiella periglandulata Pižl & Chalupský, 1984 and Parergodrilus heideri Resisinger, 1925, were recorded. For 12 enchytraeid species, DNA sequences are presented for the first time: these include, apart from the new species, further taxa such as species of Xetadrilus, a genus of which no sequences were previously available.

scholarly journals Rickettsia species infecting Amblyomma ticks from an area endemic for Brazilian spotted fever in Brazil

2011 ◽  
Vol 20 (4) ◽  
pp. 308-311 ◽  
Author(s):  
Elizângela Guedes ◽  
Romário Cerqueira Leite ◽  
Richard Campos Pacheco ◽  
Iara Silveira ◽  
Marcelo Bahia Labruna
Keyword(s):  
Dna Sequences ◽  
Spotted Fever ◽  
Rickettsial Infection ◽  
Free Living ◽  
Rickettsia Species ◽  
Rickettsia Rickettsii ◽  
New Genotype ◽  
Pcr Products ◽  
Brazilian Spotted Fever ◽  
First Time

This study reports rickettsial infection in Amblyomma cajennense and Amblyomma dubitatum ticks collected in an area of the state of Minas Gerais, Brazil, where Brazilian spotted fever is considered endemic. For this purpose, 400 adults of A. cajenennse and 200 adults of A. dubitatum, plus 2,000 larvae and 2,000 nymphs of Amblyomma spp. were collected from horses and from the vegetation. The ticks were tested for rickettsial infection through polymerase chain reaction (PCR) protocols targeting portions of three rickettsial genes (gltA, ompA, and ompB). Only two free-living A. cajennense adult ticks, and four pools of free-living Amblyomma spp. nymphs were shown to contain rickettsial DNA. PCR products from the two A. cajennense adult ticks were shown to be identical to corresponding sequences of the Rickettsia rickettsii strain Sheila Smith. DNA sequences of gltA-PCR products of the four nymph pools of Amblyomma spp. revealed a new genotype, which was shown to be closest (99.4%) to the corresponding sequence of Rickettsia tamurae. Our findings of two R. rickettsii-infected A. cajennense ticks corroborate the endemic status of the study area, where human cases of BSF were reported recently. In addition, we report for the first time a new Rickettsia genotype in Brazil.

scholarly journals Hidden in our pockets: building of a DNA barcode library unveils the first record of Myotis alcathoe for Portugal

2020 ◽  
Vol 8 ◽  
Author(s):  
Hugo Rebelo ◽  
Sónia Ferreira ◽  
Francisco Amorim ◽  
Pedro Horta ◽  
Helena Raposeira ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Dna Barcode ◽  
First Record ◽  
The Other ◽  
Index Numbers ◽  
Vast Array ◽  
First Time ◽  
Nyctalus Noctula

The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (Chiroptera) dataset containing DNA sequences of 63 specimens representing the 25 bat species currently known for continental Portugal. For that, we sequenced tissues samples obtained in a vast array of projects spanning the last two decades. We added four new Barcoding Index Numbers (BINs) to existing Chiroptera barcodes on BOLD, two belonging to Myotis escalerai, one to Plecotus auritus and the other to Rhinolophus hipposideros. Surprisingly, one of the samples initially identified in the field as Myotis mystacinus turned out to be Myotis alcathoe, which represents the first record of this species for Portugal. The presence of Nyctalus noctula in Portugal was also genetically confirmed for the first time. This case study shows the power and value of DNA barcoding initiatives to unravel new data that may be hidden on biological collections.

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