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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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    Assessment of the behaviour and survival of nematodes under low oxygen concentrations
    (Public Library Science, 2018) Kitazume, Hiromi; Dayı, Mehmet; Tanaka, Ryusei; Kikuchi, Taisei
    Oxygen is required for the completion of almost all known metazoan lifecycles, but many metazoans harbour abilities to withstand varying degrees and periods of hypoxia. Caenorhabditis elegans, one of the most popular model organism is extensively used as a model for the study of hypoxia and anoxia biology and it has been found that this nematode is capable of tolerance to varying degrees of hypoxia. Considering the extremely high diversity of nematodes, the effects of low oxygen concentration and mechanisms of adaptation to oxygen depletion differ among species. In this study, we used a simple assay to examine anoxia tolerance in four nematode species, including three free-living and one plant parasitic nematode. We found that the plant parasitic nematode Bursaphelenchus xylophilus can survive more than 14 days under anoxic conditions. Comparisons of behaviour during anoxia induction and the repertoire of oxygen sensation genes among the tested species suggested the existence of different oxygen sensation systems between B. xylophilus and C. elegans, which quickly introduce suspended animation in response to oxygen depletion to survive long-term anoxia.
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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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    Development and validation of SSR markers for the plant-parasitic nematode Subanguina moxae using genome assembly of Illumina pair-end reads
    (Brill Academic Publishers, 2015) Takeuchi, Tomoaki; Yamaguchi, Madoka; Tanaka, Ryusei; Dayı, Mehmet; Ogura, Nobuo; Kikuchi, Taisei
    Subanguina moxae, belonging to the subfamily Anguininae, is an obligate parasite of Artemisia plants, which are widely used as cooking herbs and in traditional medicine in East Asia. Because the nematode is distributed throughout East Russia and East Asia, there is concern about the potential for significant damage to commercial farming; however, details about its biology remain unclear. To investigate the genetic diversity of S. moxae, we developed 2243 simple sequence repeat (SSR) markers using Illumina short reads of the genomic DNA. We validated 100 randomly selected markers indicating their robustness and examined polymorphisms among nematode populations sampled from four different locations in Japan. These SSR markers will be a useful tool for understanding the population structure and transmission patterns of this parasitic nematode.
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    Differentially Expressed Genes Associated with Body Size Changes and Transposable Element Insertions between Caenorhabditis elegans and Its Sister Species, Caenorhabditis inopinata
    (Oxford Univ Press, 2023) Kawahara, Kazuma; Inada, Taruho; Tanaka, Ryusei; Dayi, Mehmet; Makino, Takashi; Maruyama, Shinichiro; Kikuchi, Taisei
    Why the recently discovered nematode Caenorhabditis inopinata differs so greatly from its sibling species Caenorhabditis elegans remains unknown. A previous study showed that C. inopinata has more transposable elements (TEs), sequences that replicate and move autonomously throughout the genome, potentially altering the expression of neighboring genes. In this study, we focused on how the body size of this species has evolved and whether TEs could affect the expression of genes related to species-specific traits such as body size. First, we compared gene expression levels between C. inopinata and C. elegans in the L4 larval and young adult stages-when growth rates differ most prominently between these species-to identify candidate genes contributing to their differences. The results showed that the expression levels of collagen genes were consistently higher in C. inopinata than in C. elegans and that some genes related to cell size were differentially expressed between the species. Then, we examined whether genes with TE insertions are differentially expressed between species. Indeed, the genes featuring C. inopinata-specific TE insertions had higher expression levels in C. inopinata than in C. elegans. These upregulated genes included those related to body size, suggesting that these genes could be candidates for artificial TE insertion to examine the role of TEs in the body size evolution of C. inopinata.
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    Nearly Complete Genome Assembly of the Pinewood Nematode Bursaphelenchus xylophilus Strain Ka4C1
    (Amer Soc Microbiology, 2020) Dayi, Mehmet; Sun, Simo; Maeda, Yasunobu; Tanaka, Ryusei; Yoshida, Akemi; Tsai, Isheng Jason; Kikuchi, Taisei
    Bursaphelenchus xylophilus has been destroying pine forests in East Asia and western Europe. Here, we report its nearly complete genomic sequence containing five similar to 12-Mb scaffolds and one similar to 15-Mb scaffold representing six chromosomes. Large repeat regions that were previously unidentified are now reasonably integrated, particularly in the similar to 15-Mb scaffold.
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    Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle
    (Nature Publishing Group, 2019) Tanaka, Suguru E.; Dayı, Mehmet; Maeda, Yasunobu; Tsai, Isheng J.; Tanaka, Ryusei; Bligh, Mark; Kikuchi, Taisei
    The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease, one of the most devastating forest diseases in East Asian and West European countries. The lifecycle of B. xylophilus includes four propagative larval stages and gonochoristic adults which are involved in the pathogenicity, and two stages of dispersal larvae involved in the spread of the disease. To elucidate the ecological roles of each developmental stage in the pathogenic life cycle, we performed a comprehensive transcriptome analysis using RNA-seq generated from all developmental stages of B. xylophilus and compared transcriptomes between stages. We found more than 9000 genes are differentially expressed in at least one stage of the life cycle including genes involved in general nematode biology such as reproduction and moulting but also effector genes likely to be involved in parasitism. The dispersal-stage transcriptome revealed its analogy to C. elegans dauer and the distinct roles of the two larval stages from each other regarding survival and transmission. This study provides important insights and resources to understand B. xylophilus parasitic biology.