Ryabova, A. | 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↗

bioRxiv2024

Comparative framework and adaptation of ACME HS approach to single cell isolation from fresh-frozen endocrine tissues

Current scRNA-seq studies of solid tissues mostly rely on enzymatic dissociation of fresh samples or the fallback on nuclei isolation from frozen or partially fixed samples. However, due to the complex tissue organization or cell fragility, it could be challenging to apply these approaches to the sensitive endocrine tissues. That is, dissociating intact cells from such problematic fresh-frozen samples routinely collected by biobanks remains challenging. In this study, we adapted the acetic-methanol dissociation method - ACME High Salt (ACME HS) to effectively isolate intact single cells from fresh-frozen endocrine tumor samples, including adrenal gland neoplasms, thyroid carcinomas, and pituitary neuroendocrine tumors. We compared the ability of enzymatic, ACME HS, and nuclear isolation methods to preserve the integrity of major cell types and gene expression across 41 tissue samples of different origins. We demonstrated that ACME HS simultaneously dissociates and fixes cells, thus preserving morphology and a high RNA integrity number in problematic cell types. This finding renders the ACME HS dissociation method a valuable alternative in scRNA-seq protocols for challenging tissues where obtaining live cell suspension is difficult or impossible.

genomics↗