Lyupina, Y. | bioRxiv Science

bioRxiv2026

Chromosome-level genome assembly of the sponge Halisarca dujardinii

Halisarca dujardinii is a marine sponge known for its ability to completely regenerate via cell reaggregation. Here we present the first chromosome-level genome assembly of H. dujardinii, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C data. The final assembly spans 226.5 Mbp and is organized into 21 chromosome-scale scaffolds, representing the full nuclear genome, with an assembly N50 of 10.1 Mbp. In addition, we report the complete mitochondrial genome for H. dujardinii, assembled as a circular molecule and annotated to contain 14 protein-coding genes. We provide a comprehensive genome annotation comprising 14,565 nuclear protein-coding genes, of which 85.6% are functionally annotated, along with repetitive elements and non-coding RNAs. Transcript models were refined using extensive bulk and single-cell RNA sequencing data, enabling accurate annotation of 3' untranslated regions. This new genomic resource provides a valuable foundation for investigating the molecular basis of sponge regeneration, as well as for comparative studies of sponge evolution and marine biology.

genomics↗

bioRxiv2025

Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level

Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge associated microbiomes contribute to the health of the host organisms by defending them against invading bacteria and providing them with essential metabolites. Here we describe microbiomes of three sympatric species of cold-water marine sponges - Halichondria panicea, Halichondria sitiens, and Isodictya palmata - sampled over a period of six years at the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria illustrating varying complexity of microbiomes. On a community level, sponge associated microbiomes shared common symbiotic features; they encoded multiple eukaryotic-like proteins, biosynthetic pathways, and transporters of amino acids and vitamins essential for sponges. On a species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts indicating specialization within microbiomes. Particularly, taurine and sulfoacetate metabolism pathways were associated exclusively with dominant symbionts in all three sponge species. Our study demonstrates strong functional convergence and co-evolution of microbiomes of sympatric cold-water sponge species with a distribution of functions between community members. Additionally, we observed dramatic shifts in compositions of sponge microbiomes coinciding with abnormally high water temperatures during the 2018 season, highlighting the vulnerability of cold-water ecosystems to global warming.

microbiology↗