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

A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

Identification and a culture method for a Helicotylenchus microlobus from tomato in China

Background

The nematodes of the genus Helicotylenchus are root parasites of a wide variety of plants, and certain species can cause serious damage to their hosts. During a survey of the plant-parasitic nematode associated with tomato, a population of Helicotylenchus was collected from tomato roots and soil samples. Thus, one of the objectives of the study was to confirm the specie of Helicotylenchus obtained from the tomato samples based on morphological and molecular characteristics. In addition, a mass pure culture of plant-parasitic nematodes is key to pathogenicity studies and many other biological studies. However, a successful mass rearing method for Helicotylenchus has not been reported. Thus, the other objective of the study was to establish a method of culturing Helicotylenchus.

Results

Based on both the morphological characteristics and molecular analysis of the internal transcribed spacer (ITS) and D2-D3 expansion region of 28S ribosomal RNA (rRNA) sequences the specimens were identified as Helicotylenchus microlobus. Phylogenetic analysis with the rRNA sequences of the ITS and 28S D2-D3 regions was consistent with molecular identification, suggesting this population formed a highly supported clade with other H. microlobus populations. Additionally, a method for culture of H. microlobus on carrot disks was established, and the effect of temperature on the reproduction rate (Rr) of H. microlobus was investigated. The optimum temperature for culturing H. microlobus on carrot disks was 27.5 °C and, after inoculation with 30 females of H. microlobus at 27.5 °C for 90 days, Rr reached 406.

Conclusions

To our knowledge, this is the first detailed description of H. microlobus from tomato in China. This study also demonstrated that the carrot disk method is suitable for the culture of H. microlobus. This study lays a foundation for other related research on H. microlobus, and has significance for the study of Helicotylenchus.

An Integrated Approach for Synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) Reveals High Intraspecific Mitogenomic Variation

Rotylenchus is a widely distributed, economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters, including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of Rotylenchus goodeyi from Belgium, Poland, and the Netherlands revealed important character variations of this species, leading to synonymization of R. rhomboides with R. goodeyi and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes, each approximately 23 Kb in size, differing by approximately 9% and containing 11 protein-coding genes, 2 ribosomal RNA genes, and as many as 29 transfer RNA genes. In addition to the first representative whole-genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full-length mitogenome and the ribosomal DNA sequences of R. goodeyi.