Twinkle twinkle brittle star, how I wonder what your genes are: Ophioderma brevispinum as a genomic resource for regeneration

Abstract

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 experimtental 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 146,833 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.

EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

“…We have also added the "EchinoidDB" resource that contains the highquality genome assembly data of L. variegatus [20], a sea urchin found in shallow waters throughout the western Atlantic Ocean ranging from the United States to Venezuela. The rationale for creating these two new data resources is that there has been a growing use of these two species in recent molecular studies in developmental and regenerative biology [16,20,31,[48][49][50][51][52].…”

“…Knowledge of the Notch and Wnt signaling pathways is important because they are highly conserved in the animal kingdom and regulate a variety of cellular processes, including proliferation, differentiation, fate specification, and cell death [74][75][76][77]. Recent studies indicate that inhibiting the Notch signaling pathway prevented the brittle stars from fully regenerating their arms [16,31]. Furthermore, Wnt signaling pathway is a Fig.…”

“…To demonstrate the practical utility of the new version of EchinoDB [18] and its associated resources -Ophi-uroidDB [22] and EchinoidDB [23] -we illustrate how EchinoDB is used in retrieving key components of the Notch and Wnt signaling pathways, that are crucial for tissue regeneration in echinoderms [16,[28][29][30][31][32]. In addition, we describe the use of SequenceServer (BLAST tool) [27,33,26] integrated within EchinoDB to find the putative homologs of the skeleton matrix proteins [4,[34][35][36][37] and tensilin (a protein that controls tensile strength of mutable collagenous tissues) [5, 38-40, 41, 42], previously reported in sea urchins (Echinodermata:Echinoidea) and sea cucumbers (Echinodermata: Holothuroidea).…”

A subterminal growth zone at arm tip likely underlies life-long indeterminate growth in brittle stars

“…They are capable of quickly regrowing their arms following autotomy. The molecular underpinnings of regeneration in these animals are being actively uncovered through functional [ 10 ], cellular [ 11 ], and genomic studies [ 12 ]. Here, we focus on the growth of the intact (i.e., non-regenerating) adult arms.…”