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2022 Aug 11;231:574. doi: 10.1186/s12864-022-08750-y.
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Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research.
BACKGROUND: Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms.
RESULTS: We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration.
CONCLUSIONS: The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration.
Fig. 1. Ophioderma brevispinum, an emerging model organism in echinoderm regenerative biology. A An uninjured adult individual of O. brevispinum. B–H Regenerating arm at different time points post-injury. The regenerating distal end of the arm is to the left
Fig. 2. Simplified diagram of the Notch signaling pathway. The pathway is mediated by juxtacrine signaling that requires direct physical contact between the signaling and receptor cells. The Delta/Serrate (Jagged) ligands and Notch receptors are transmembrane proteins embedded into the plasma membrane of the signaling and receptor cells, respectively. Ligand-receptor interaction triggers conformational changes in the Notch protein that allows for proteolytic cleavage of the receptor by the ADAM metalloprotease and the multiprotein γ-secretase complex. The latter includes the catalytic component presenilin, as well as regulatory/stabilizing subunits nicastrin, Aph-1, and Pen (presenilin enhancer)-2. This proteolytic cleavage releases the Notch intercellular domain that translocates into the nucleus and activates the transcription factor RBP-J by inducing the release of co-repressors (e.g., NCOR, CIR, MINT, and HDAC) and recruitment of co-activators, such as Mastermind (MAM), p300, and NACK. The activated transcription factor complex initiates transcription of the direct targets of the pathway, including Hes and Hey. Even though the pathway itself is conceptually simple, it is subjected to a multitude of regulatory inputs at multiple levels, including receptor post-translational maturation and stability/availability of the key pathway components in both the signaling and receptor cells. One of the properties of the Notch pathway is the ability to sustain itself through a series of feed-forward loops, thus resulting in an all-or-nothing response. For example, NACK, which is a transcriptional co-activator in the pathway is itself positively regulated by Notch. The genes shown in the diagram were searched for and identified in the O. brevispinum draft genome (see Table 5). Three different searches for Notch related genes in the draft genome were performed, designated by green boxes (BLAST, Exonerate, and conserved domain search respectively), filled boxes indicate positive identification
Fig. 3. Schematic workflow of the O. brevispinum de novo DNA and RNA assembly. The main software tools used at each step of the workflow are shown in parenthesis. Grey boxes indicate four main components of the workflow. DNA: library preparation, quality control, high-throughput sequencing, and de novo assembly of gDNA. RNA: transcriptome assembly described in a previous publication. Genome size estimation: two different strategies used to estimate the haploid genome size. Repeat Masking: identification and categorization of repetitive DNA in the gDNA assembly. We used FastQC at different workflow steps to track the effect of quality control procedures on the sequence reads (see dashed arrowhead lines)
Fig. 4. The complete mitochondrial genome of Ophioderma brevispinum. Arrows indicate the main genomic features and their orientation. The blue lines indicate variation in GC content. The green lines indicate variation in AT content
Fig. 5. Schematic workflow of the procedures used for gene prediction and annotation of the O. brevispinum draft genome. Main steps (indicated by the grey boxes) are named according to the leading software used on each stage (BRAKER; BLAST; and exonerate, GMAP, and BLAT)