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Genome Biol
2025 Mar 31;261:82. doi: 10.1186/s13059-025-03542-5.
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Chromosome-level genome assembly and single-cell analysis unveil molecular mechanisms of arm regeneration in the ophiuroid Ophiura sarsii vadicola.
Xu QZ
,
Li YX
,
Shi WG
,
Dong Y
,
Li Z
,
Ip JC
,
Galaska MP
,
Han C
,
Zhang Q
,
Sun YY
,
Zhao LL
,
Sun KM
,
Wang ZL
,
Qiu JW
,
Zhang XL
.
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BACKGROUND: Ophiuroids, belonging to Ophiuroidea in Echinodermata, possess remarkable regenerative capacities in their arms, relying on cellular recruitment and de-differentiation. However, limited high-quality genomic resources have hindered the investigation of the underlying molecular mechanisms of ophiuroid regeneration.
RESULTS: Here, we report a chromosome-level genome of Ophiura sarsii vadicola, 259.28 Mbp in length with a scaffold N50 length of 66.91 Mbp. We then perform bulk and single-cell RNA sequencing analysis to investigate gene expression and cellular dynamics during arm regeneration. We identify five distinct cellular clusters involved in the arm regeneration and infer the dynamic transformations from sensory stimulation to injury response, wound healing, and tissue regeneration. We find that progenitor cells derived from connective tissue cells differentiate into muscle, cartilage, endothelial, and epithelial cells. Pseudotime analysis indicates that muscle differentiation occurs early in the regeneration process.
CONCLUSIONS: Our genomic resource and single-cell atlas shed light on the mechanisms of organ regeneration in ophiuroids.
Fig. 1. Genomic features of Ophiura sarsii vadicola and phylogenetic relationships among echinoderms with available genome data. A Circos plot of Ophiura sarsii vadicola genomic features with an image of an O. sarsii vadicola specimen (5 cm in size). Circles show (1) the length of each chromosome, (2) the density of genes, (3) the density of repetitive sequences, and (4) GC content. B Phylogenetic relationships and divergence times of ten echinoderms with genome resources. A yellow asterisk marks the node where time calibration was applied for divergence time analysis. The pie diagram (orange and blue) shows the percentage of expanded and contracted gene families for each tip species. C Collinearity relationships between O. sarsii vadicola (Osav) and O. sarsii (Osar), and between O. sarsii vadicola and Amphiura filiformis (Afil)
Fig. 2. Arm regeneration and differential gene expression in O. sarsii vadicola at four post-amputation time points. A Histological observations of the arm tip of O. sarsii vadicola on day 13 post-amputation. N: nerve tissue, M: muscle tissue, V: vertebral structure. B Zoomed-in view of the blastema from A. N: nerve tissue, b: blastema, RWC: radial water canal, ACC: aboral coelomic cavity, ct: connective tissue. C Principal component analysis (PCA) of gene expression profiles at four time points during regeneration. D Up- and downregulated gene expression at day 13 compared to earlier time points. E Annotation and enrichment analysis of differentially expressed genes at day 13 post-amputation compared to earlier time points
Fig. 3. Cell type annotations of O. sarsii vadicola arm tips at various time points based on scRNA-seq data. A Bar plot showing cell number proportions. B
t-distributed stochastic neighbor embedding (t-SNE) diagram for the single-cell RNA of O. sarsii vadicola. Each point represents a cell with circles highlighting CT I and CT II cells. C Expression levels of cell type marker genes within the six clusters. Circle sizes indicate the proportion of cells in each cluster expressing a given gene, while the color reflects the mean expression across those cells. D Expression levels of marker genes across the six cell clusters at various time points (X-axis), with the Y-axis showing expression levels
Fig. 4. Clustering results and marker gene expression for CT I (A, C) and CT II (B, D) cells, with a hypothesis of cellular mechanisms during O. sarsii vadicola arm regeneration (E)
Fig. 5. Pseudotiming analysis of CT I and CT II cells during regeneration. A Pseudotime ordering of cells. B Differentiation status of each branch. C Distribution of each cell group along the pseudotime axis. D Marker gene expression in cell subgroups over pseudotime. E Expression of Lrp6 and VEGF over pseudotime, with the X-axis showing pseudotime and the Y-axis showing expression levels
