Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species

Bai, Mengxin; Xue, Qiao; Qiao, Kaikai; Ning, Xulan; Xiao, Shun; Cheng, Xi; Liu, Guokun

doi:10.21307/jofnem-2020-038

Cited by 13 publications

(11 citation statements)

References 33 publications

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“…The nematode family Tylenchidae Örley [1] is exceptionally diverse in soil habitats. Members of this family have high ecological significance and prominence in both agricultural and natural systems [2][3][4]. Based on their life cycle strategies, Tylenchidae species have been given a colonizer-persister (cp) value of 2 [5].…”

Section: Introductionmentioning

confidence: 99%

First Report of Three Tylenchidae Taxa from Southern Alberta, Canada

2021

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Members of the family Tylenchidae are highly abundant in soil habitats, including agricultural settings, where they play key ecological roles. In the present study, we identified three Tylenchidae species, namely Basiria bhabi, Coslenchus acceptus, and Filenchus vulgaris, using integrative taxonomy. The detailed morphological and morphometric characteristics, distribution, and host associations of each species were also discussed. Phylogenetic analyses of these populations with other Tylenchidae nematodes indicated the presence of divergent lineages in Filenchus and Basiria, whereas Coslenchus appeared to be a monophyletic genus. Herein, we aim to grow awareness about this common but least studied group of nematodes. The species reported in this study are new records for Canada, revealing that the identified nematode diversity in our cultivated areas is relatively underrepresented. Our analyses also provided greater taxonomic resolution and captured rare taxa that might have been missed or misidentified in prior nematode inventory surveys. These findings will add to our understanding of the nematofauna of southern Alberta, thereby providing a more complete picture of existing nematode diversity present in the fields of this highly cultivated region.

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Section: Introductionmentioning

confidence: 99%

First Report of Three Tylenchidae Taxa from Southern Alberta, Canada

2021

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“…Phylogenetic tree was generated with a Bayesian inference method using MrBayes 3.2.6 ( Huelsenbeck and Ronquist, 2001 ; Ronquist et al, 2012 ). Aphelenchus avenae Bastian, 1865 (KP527123) was chosen as outgroup for the tree according to ( Bai et al, 2020 ; Hosseinvand et al, 2020b ; Yaghoubi et al, 2015 ). The analysis under general time-reversible model of sequence evolution with correction for invariable sites and a gamma-shaped distribution (GTR + I + G) model was initiated with a random starting tree and run with the Markov Chain Monte Carlo (MCMC) for 1 × 10 6 generations.…”

Section: Methodsmentioning

confidence: 99%

Morphological and molecular characterization of two species of Neothada Khan, 1973 (Nematoda: Tylenchidae) from Iran, with notes on N. cancellata

Hosseinvand

Eskandari

Ghaderi

2021

Journal of Nematology

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Three species of the genus Neothada , including N. cancellata, N. hades and N. major , collected from the rhizosphere of mosses in Khuzestan, southwestern Iran, are redescribed and illustrated. Neothada hades and N . major are new records from Iran. Neothada hades has 14 longitudinal incisures excluding the lateral field, body length of 586 (505–674) µm, stylet 10.5 (10.0–10.8) µm in length bearing distinct basal knobs, and an elongated-conical tail 70.4 (65–74) µm long with a finely to bluntly rounded terminus. N. major possesses 18–20 longitudinal incisures excluding the lateral field, body length of 657 (600–728) µm, stylet 10.9 (10.3–11.7) µm long with basal swellings but not distinct knobs, and an elongated-conical tail 78.2 (70–83) µm long ending to a finely to bluntly rounded terminus. Molecular phylogenetic studies of the two species ( N. hades and N. major ) with 664 bp of D2-D3 expansion segments of 28 S rDNA revealed that they form a clade with N . cancellata .

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“…COI is also a reference for soil microarthropods (Porter et al ., 2019 ). Although priming regions are too variable to be used to scan all nematode diversity (Ahmed et al ., 2019 ), COI is a promising marker to delimit species within nematode families (Bai et al ., 2020 ). In soil protist metabarcoding, this marker was applied to Arcellinida (lobose testate amoebae) revealing niche differentiation between closely related species (Singer et al ., 2018 ).…”

Section: Future Perspectives On Eukaryotic Metabarcoding In Soilsmentioning

confidence: 99%

Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA‐based studies

Lara

Geisen

2022

Environmental Microbiology

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Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.

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Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species

Cited by 13 publications

References 33 publications

First Report of Three Tylenchidae Taxa from Southern Alberta, Canada

First Report of Three Tylenchidae Taxa from Southern Alberta, Canada

Morphological and molecular characterization of two species of Neothada Khan, 1973 (Nematoda: Tylenchidae) from Iran, with notes on N. cancellata

Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA‐based studies

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