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    Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis
    (Nature Research, 2021) Dayi, Mehmet; Kanzaki, Natsumi; Sun, Simo; Ide, Tatsuya; Tanaka, Ryusei; Masuya, Hayato; Kikuchi, Taisei
    Caenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.
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    The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus
    (Bmc, 2022) Sun, Simo; Kanzaki, Natsumi; Dayı, Mehmet; Maeda, Yasunobu; Yoshida, Akemi; Tanaka, Ryusei; Kikuchi, Taisei
    Background The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. Results In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. Conclusions The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.
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    Preliminary survey of nematodes associated with broadleaved trees in Izmit Forest Management Directorate, Turkey
    (Wiley, 2020) Tasdemir, Sinan; Akbulut, Suleyman; Kanzaki, Natsumi; Ozturk, Nuray
    A survey for Bursaphelenchus species was carried out in broadleaf forest sites of Izmit Forest Management Directorate. Nematodes were extracted from 128 wood samples, and 22 of them were cultured. Nematodes were identified using morphological characteristics and molecular analysis by amplifying D2-D3 LSU with primers. Only one Bursaphelenchus species, Bursaphelenchus mucronatus kolymensis, was isolated from Quercus petraea representing the first report from broadleaved tree species in Turkey. Paraphelenchus acontioides and Aphelenchoides heidelbergi were identified and presented herein as the first reports of these two species from Turkey. In addition, five Aphelenchoides species were also found and reported as Aphelenchoides sp.
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    Reverse taxonomy reveals Pristionchus maupasi (Diplogasterida: Diplogastridae) association with the soil-dwelling bee Andrena optata (Hymenoptera: Andrenidae) in Turkey
    (Florida Entomological Soc, 2015) Hazır, Canan; Kanzaki, Natsumi; Gülcü, Barış; Hazır, Selçuk; Giblin-Davis, Robin M.
    Previous molecular operational taxonomic unit (MOTU) survey work with diplogastrid dauers from the abdominal glands of adult female soil- dwelling andrenid bees in Turkey had suggested commensal relationships between species of the genus Andrena and a new species of Koerneria and several species from an unidentified nematode clade near "Mononchoides" (based upon comparisons with GenBank at the time). We used reverse taxonomy on dauer nematodes from Andrena optata from Turkey to successfully culture, morphotype, and sequence adult nematodes that fully matched Pristionchus maupasi and one of the MOTUs previously isolated as dauers from the abdominal glands of A. limata and A. flavipes, and previously designated as belonging to the clade near "Mononchoides." This study demonstrates the value of reverse taxonomy for resolving MOTU identification issues as the depth of the reference sequence database increases and successful cultures or environmental samples of adults are made available for morphotypic and genotypic comparisons. In addition, it has helped expand our knowledge of the potential host range and biogeographical distribution of P. maupasi which was originally thought to be relatively host specific on scarab beetles, and has raised questions about the chemical ecology of dauers for this species in the wild.