bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.01.15.699767

The genome of an enigmatic sea urchin parasite Echinomermella matsi Jones & Hagen, 1987 resolves its place among other invertebrate parasitic nematodes

KIRANGWA, J.·King, E.·Collins, J.·Bates, A.·Blaxter, M. L.·Holovachov, O.
View original source ↗Export metadata ↓

Abstract

We present a genome of Echinomermella matsi (Nematoda: Plectida: Benthimermithidae), a body cavity parasite of the green sea urchin Strongylocentrotus spp. commonly found along the coast of Central and Northern Norway. Three assemblies were generated, one from multiple individuals using Oxford Nanopore long read data and two from two individuals using PacBio long read data. The genome of Echinomermella matsi is 65 Mb long consisting of 7 chromosomes, with nematode Benchmarking Using Single Copy Orthologue (BUSCO) completeness reaching 61%. The E. matsi chromosome complement corresponds to the proposed Rhabditida ancestral linkage groups. Phylogenetic analyses using newly generated 18S rRNA genes and a multigene dataset consisting of BUSCO protein coding genes, supported by morphological observations of juveniles, firmly place Echinomermella within the nematode order Plectida, alongside nematode parasitoids of marine invertebrates, Trophomera or Neocamacolaimus. As a result, the generally free-living order Plectida includes at least three independently evolved lineages of nematodes symbiotic with various groups of aquatic and terrestrial invertebrates and with unicellular organisms. This, and the fact that Plectida is the closest sister lineage to Rhabditida as a whole, and one node away from the exclusively animal parasitic Spirurina, makes this lineage a valuable model for study of evolution of animal parasitism in the aquatic environment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/699767v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@d44b08org.highwire.dtl.DTLVardef@18a3310org.highwire.dtl.DTLVardef@1e79dforg.highwire.dtl.DTLVardef@d33b3b_HPS_FORMAT_FIGEXP M_FIG C_FIG Article summaryThe researchers generated a genome of Echinomermella matsi, a body cavity parasite of the green sea urchin, using PacBio and Oxford Nanopore long read sequencing. The genome is 65 Mb long, shows 61% of nematode BUSCO completeness, and consists of 7 chromosomes. Single and multiple gene phylogenies place Echinomermella within mostly free-living Plectida as one of the three independently evolved parasitic lineages. The authors suggest Echinomermella to be a valuable model to study evolution of animal parasitism in the aquatic environment. The genome can be used to develop biocontrol strategies of Echinomermella in mariculture of green sea urchin.

Source connections

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

KIRANGWA, J., King, E., Collins, J., Bates, A., Blaxter, M. L., Holovachov, O.. 2026-01-16. The genome of an enigmatic sea urchin parasite Echinomermella matsi Jones & Hagen, 1987 resolves its place among other invertebrate parasitic nematodes. https://doi.org/10.64898/2026.01.15.699767

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗