Biology subjects

Oomura, S.

Publications and source records attributed to Oomura, S..

4 recordsLinked to original sources

bioRxiv2026

Divergence of Cortical Force-Generating Mechanisms Underlies Differences in Spindle Behavior between C. elegans and C. inopinata

Microtubule-dependent pronuclear migration and mitotic spindle positioning are fundamental processes during the first embryonic division in many animals. In the one-cell embryo of Caenorhabditis elegans, these events are regulated by well-characterized pulling forces acting on astral microtubules, including cortical forces mediated by the G-GPR-LIN-5 dynein complex. Although the overall framework of these dynamics is conserved, recent studies have revealed substantial interspecies variation in their regulation. Here, we investigated nuclei and mitotic spindle behaviors in one-cell embryos of Caenorhabditis inopinata, the closest known relative of C. elegans, using live-cell imaging and functional perturbation. We found that C. inopinata embryos exhibit altered pronuclear migration, reduced anaphase spindle oscillations, and slower centrosome diffusion during telophase compared with C. elegans. These differences suggest weaker cortical pulling forces. Functional analyses using RNA interference showed that GPR retains its essential role in force generation, whereas the contribution of the microtubule depolymerizing kinesin KLP-7 is reduced in C. inopinata. Our results point to evolutionary changes in microtubule-regulated spindle dynamics, and provide insight into how conserved cellular processes can diversify through subtle changes in their underlying mechanisms.

cell biology↗

bioRxiv2026

Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome

BackgroundTransposable elements (TEs) serve as powerful drivers of genome innovation but also threaten genome integrity. The PIF/Harbinger superfamily is distinctive among DNA transposons because mobilisation typically requires proteins, a DDE transposase and a MADF DNA-binding protein. Caenorhabditis inopinata, the closest known relative of C. elegans, has a TE-rich genome and lacks multiple components of the ERGO-1-class endogenous small-RNA pathway, making it a useful system for examining TE dynamics in a distinct host context. We identified a spontaneous dumpy mutant of C. inopinata caused by insertion of a PIF/Harbinger-family element into the coding region of Cin-dpy-11. The inserted element, designated Harbinger-1M_cIno, belongs to the Turmoil2 lineage originally defined in C. elegans and retains a MADF domain but lacks a recognisable DDE transposase ORF. Genome-wide curation recovered 258 related copies, revealing a strongly asymmetric family structure. Short noncoding derivatives were predominant, MADF-bearing derivatives were expanded and only one DDE-bearing locus retained an apparently intact transposase gene, suggesting that DDE and MADF functions are partitioned across distinct elements and may be supplied in trans during mobilisation. We also identified a second PIF/Harbinger-derived family, Harbinger-2M_cIno, associated with the Turmoil1 lineage. This family comprises 1,376 copies and therefore records substantial past amplification, but it lacks a detectable DDE source, shows greater sequence divergence and more degraded terminal structures than Harbinger-1M_cIno. Together, these data indicate that the two PIF/Harbinger lineages in C. inopinata differ not in whether amplification occurred, but in when it occurred and whether present-day mobilisation competence has been retained.

genetics↗

bioRxiv2026

A Fluorescent Dauer Marker in Caenorhabditis inopinata Enables Comparative Analysis of Dauer-Inducing Mechanisms

Dauer larvae are a dormant developmental stage in nematodes that is induced by a range of environmental cues. The molecular mechanisms that transduce these cues to regulate dauer entry have been well characterized in Caenorhabditis elegans, whereas those in other nematode species remain unclear. The closest known sibling species of C. elegans, Caenorhabditis inopinata, occupies a distinct ecological niche and shows an extremely low frequency of dauer formation by starvation in laboratory conditions, suggesting that it could serve as a useful comparative model for analyzing dauer-inducing mechanisms. To support such analysis, we generated a fluorescent dauer reporter, Cin-col-183p::mCherry, in C. inopinata based on a previously reported dauer-specific reporter in C. elegans. This reporter showed fluorescence specifically in the pre-dauer and dauer stages, but not in other developmental stages, indicating that it functions as a dauer-specific marker in C. inopinata. Using these marker strains, we compared the responses to high temperature and RNAi-mediated knockdown of insulin/IGF-1 pathway genes (daf-2, age-1, and pdk-1), and found that dauer induction differs mechanistically between C. elegans and C. inopinata. This dauer-specific fluorescent strain will be a useful tool for investigating the diversity of dauer-inducing mechanisms across nematode species. Article SummaryDauer is a dormant developmental stage in nematodes induced by environmental stress. Although its regulation is well studied in Caenorhabditis elegans, the mechanisms in other species remain unclear. Here, we developed a fluorescent dauer reporter, Cin-col-183p::mCherry, in Caenorhabditis inopinata, a close relative of C. elegans. The reporter was specifically expressed in pre-dauer and dauer stages, confirming its usefulness as a dauer marker. Using this strain, we found that responses to high temperature and insulin/IGF-1 pathway gene knockdown differ between C. elegans and C. inopinata. This reporter will help reveal diversity in dauer-inducing mechanisms across nematode species.

developmental biology↗

bioRxiv2024

Dramatic evolutionary changes of conserved noncoding elements accompanied by extraordinary features of Caenorhabditis inopinata

Phenotypic evolution is driven by genetic mutations occurring in both protein-coding and noncoding regions of the genome. Conserved noncoding elements (CNEs) have--at least partially--gene regulatory functions and contribute to the evolution of organisms by altering their gene expression. Evolutionary changes in CNEs, including their loss and accelerated evolution, can play crucial roles in shaping species-specific traits. The extensive functional genomic information available for the model nematode Caenorhabditis elegans, together with the recent accumulation of high-quality genome sequences from related species, has made Caenorhabditis nematodes a powerful system for comparative genomics focused on CNE evolution. The recently described species Caenorhabditis inopinata has several peculiar traits notable for its unusually large body size and is regarded as an appropriate species that links phenotypic evolution with genomic changes. Here, using comparative genomics and transcriptomics in C. inopinata, we analyzed the evolution of CNEs and inferred their influence during phenotypic evolution. We detected substantial evolutionary changes in CNEs in C. inopinata compared to other relatives--changes frequently associated with body morphology and behavior corresponding to distinct ecological traits. Our findings suggest that loss and accelerated evolution of CNE are associated with species-specific traits and provide new insight into the impact of noncoding elements on evolution. Significance statementLarge-scale phenotypic evolution has been observed across a wide range of taxa and may be accompanied by substantial genomic changes. Caenorhabditis inopinata, a nematode species closely related to C. elegans, shows several distinctive morphological and behavioral traits compared with its congeners, and through comparative genomics and transcriptomics, we identify substantial evolutionary changes in conserved noncoding elements (CNEs)-- including their loss and accelerated sequence evolution. Furthermore, these changes are frequently associated with genes involved in morphology and behavior, suggesting a potential link between CNE evolution and species-specific phenotypes.

evolutionary biology↗