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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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    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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    piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode
    (Nature Portfolio, 2022) Suleiman, Mona; Kounosu, Asuka; Murcott, Ben; Dayı, Mehmet; Pawluk, Rebecca; Yoshida, Akemi; Viney, Mark
    The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5 ' uridine (21-22Us) and a 5 ' monophosphate, and (ii) 27 nt long sRNAs with a 5 ' guanine/adenine (27GAs) and a 5 ' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
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    Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies
    (Royal Soc, 2024) Kounosu, Asuka; Sun, Simo; Maeda, Yasunobu; Dayi, Mehmet; Yoshida, Akemi; Maruyama, Haruhiko; Hunt, Vicky
    The Strongyloides clade, to which the parasitic nematode genus Strongyloides belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites. Reproductive strategies are also diverse in this group of nematodes, employing not only sexual reproduction but also parthenogenesis, making it an attractive group to study genome adaptation to specific conditions. An in-depth understanding of genome evolution, however, has been hampered by fragmented genome assemblies. In this study, we generated chromosome-level genome assemblies for two Strongyloides species and the outgroup species Rhabditophanes diutinus using long-read sequencing and high-throughput chromosome conformation capture (Hi-C). Our synteny analyses revealed a clearer picture of chromosome evolution in this group, suggesting that a functional sex chromosome has been maintained throughout the group. We further investigated sex chromosome dynamics in the lifecycle of Strongyloides ratti and found that bivalent formation in oocytes appears to be important for male production in the mitotic parthenogenesis.This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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    Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1
    (Amer Soc Microbiology, 2020) Sun, Simo; Shinya, Ryoji; Dayi, Mehmet; Yoshida, Akemi; Sternberg, Paul W.; Kikuchi, Taisei
    Bursaphelenchus okinawaensis is a self-fertilizing, hermaphroditic, fungus-feeding nematode used as a laboratory model for the genus Bursaphelenchus, which includes the important pathogen Bursaphelenchus xylophilus. Here, we report the nearly complete genome sequence of B. okinawaensis. The 70-Mbp assembly contained six scaffolds (>11 Mbp each) with telomere repeats on their ends, indicating complete chromosomes.