mtCOI successfully diagnoses the four main plant-parasitic Aphelenchoides species (Nematoda: Aphelenchoididae) and supports a multiple origin of plant-parasitism in this paraphyletic genus

Sánchez-Monge, Alcides; Janssen, Toon; Fang, Yiwu; Couvreur, Marjolein; Karssen, Gerrit; Bert, Wim

doi:10.1007/s10658-016-1141-1

Cited by 27 publications

(10 citation statements)

References 49 publications

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“…( Kanzakiand and Giblin-Davis, 2012 ; Ye et al, 2007 ), Aphelenchoides spp. ( Sánchez-Monge et al, 2017 ; Xu et al, XXXX ), Meloidogyne spp. ( Kiewnick et al, 2014 ), Pratylenchus spp.…”

Section: Discussionmentioning

confidence: 99%

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

Bai

Xue

Qiao

et al. 2020

Journal of Nematology

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Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships.

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“…( Kanzakiand and Giblin-Davis, 2012 ; Ye et al, 2007 ), Aphelenchoides spp. ( Sánchez-Monge et al, 2017 ; Xu et al, XXXX ), Meloidogyne spp. ( Kiewnick et al, 2014 ), Pratylenchus spp.…”

Section: Discussionmentioning

confidence: 99%

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

Bai

Xue

Qiao

et al. 2020

Journal of Nematology

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“…The mitochondrial DNA region encoding for mtCOI gene has been widely explored for barcoding application purposes in many animal organisms (Rach et al, 2017). It was also used in Hoplolaimidae and other nematode groups (Kanzaki and Futai, 2002;Derycke et al, 2010;Riepsamen et al, 2011;Gutiérrez-Gutiérrez et al, 2012;Kumari and Subbotin, 2012;van den Berg et al, 2013;Holguin et al, 2015;van den Berg et al, 2017;Sanchez-Monge et al, 2017;Skwiercz et al, 2017). In this study, to enhance the process of delineation and species identification within genus Helicotylenchus, which was underrepresented in terms of available mtCOI sequences, a new set of mtCOI primers was developed and tested.…”

Section: Hoplolaimus Galeatus (Eu626787)mentioning

confidence: 99%

Phylogenetic studies on three Helicotylenchus species based on 28S rDNA and mtCOI sequence data

Rybarczyk-Mydłowska

Dmowska

Kowalewska

2019

Journal of Nematology

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To facilitate the process of spiral nematode species delineation, populations of Helicotylenchus canadensis, H. pseudorobustus, and H. varicaudatus deriving from various locations and diverse natural and anthropogenic environments from Poland were investigated and characterized. For the first time, 28S rDNA sequences are reported for H. canadensis and H. varicaudatus, whereas new mtCOI sequences were acquired for all three analyzed species. A Bayesian phylogenetic analysis of the 28S rDNA fragments revealed that H. canadensis and H. varicaudatus are members of a clade that is a sister group to all other Helicotylenchus species; however, the closest known sister group to H. canadensis is H. vulgaris type A. Both 28S rDNA-and mtCOI-based phylogenetic results suggest that this clade excludes H. pseudorobustus, whose most recent common ancestor with the former species was inferred to be the ancestor of all Helicotylenchus species. Moreover, within the mtCOI sequences obtained from H. pseudorobustus, unlike from the other two, a simultaneous presence of TAG and TAA codons was identified. This may indicate mitochondrial genetic code alterations or other genomic rearrangements in H. pseudorobustus.

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“…The COI gene has been shown to provide a greater taxonomic resolution than the small subunit (18S rRNA) rDNA [17]. The potential of COI gene-based barcoding specific to particular groups of nematodes has been explored on pure DNA samples of various nematode taxa including root-knot nematodes [18], marine nematodes [16], Aphelenchoididae [19] and Pratylenchus [20]. A lack of suitable COI-based consensus primers for the detection of nematode diversity in comparison to 18S-based primers limits the implementation of COI-based metabarcoding for nematodes [21].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities

et al. 2020

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While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step.

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mtCOI successfully diagnoses the four main plant-parasitic Aphelenchoides species (Nematoda: Aphelenchoididae) and supports a multiple origin of plant-parasitism in this paraphyletic genus

Cited by 27 publications

References 49 publications

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

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

Phylogenetic studies on three Helicotylenchus species based on 28S rDNA and mtCOI sequence data

Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities

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