Little skate genome provides insights into genetic programs essential for limb-based locomotion

Abstract

The little skate Leucoraja erinacea, a cartilaginous fish, displays pelvic fin driven walking-like behavior using genetic programs and neuronal subtypes similar to those of land vertebrates. However, mechanistic studies on little skate motor circuit development have been limited, due to a lack of high-quality reference genome. Here, we generated an assembly of the little skate genome, with precise gene annotation and structures, which allowed post-genome analysis of spinal motor neurons (MNs) essential for locomotion. Through interspecies comparison of mouse, skate and chicken MN transcriptomes, shared and divergent gene expression profiles were identified. Comparison of accessible chromatin regions between mouse and skate MNs predicted shared transcription factor (TF) motifs with divergent ones, which could be used for achieving differential regulation of MN-expressed genes. A greater number of TF motif predictions were observed in MN-expressed genes in mouse than in little skate. These findings suggest conserved and divergent molecular mechanisms controlling MN development of vertebrates during evolution, which might contribute to intricate gene regulatory networks in the emergence of a more sophisticated motor system in tetrapods.

TheIroquois(Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development

“…Here, we show that members of the Irx homeobox gene family are expressed in worm, mouse and human MNs, consistent with previous C. elegans studies and mouse transcriptomic datasets 67,71,80 . Further, Irx genes are expressed in MNs of the little skate, Leucoraja erinacea , a marine species of jawed vertebrates, sharing a common ancestor with tetrapods 81 . The remarkable conservation in Irx MN expression suggests critical functions.…”

Description of a Remarkable New Skate Species of Leucoraja Malm, 1877 (Rajiformes, Rajidae) from the Southwestern Indian Ocean: Introducing 3D Modeling as an Innovative Tool for the Visualization of Clasper Characters

“…Snout very long, tip pointed; snout angle about 65° (69-85°), the narrower angle in larger specimens; preorbital length 21.6% (17.2-22.3%) TL, 6.4 (4.5-6.8) times interorbital width, and 2.5 (2.4-3.1) times in disc width (Fig- ures 5 and 6). Orbits moderately large, diameter 1.1 (1.0-1.2) times interorbital width and 16.7% (16.5-23.6%) of preorbital snout length; spiracle proper aperture length 70.3% (59.4-71.4%) of orbit horizontal diameter; interspiracular space 1.6 (1.6-1.9) times interorbital width; 13 (12)(13)(14) pseudobranchial folds in each spiracle (Figure 7). Tail solid, broadly depressed, gradually tapering to tip; length from mid-vent to tip 0.9 (0.8-1.2) times body length from snout tip to mid-vent and 46.8% (47.5-53.6%) TL; ratio tail width to height at level of pelvic tips 1.8 (1.8-1.9) and at level of first dorsal-fin origin 2.0 (1.4-2.2) (Figures 8 and 9).…”

“…Although several studies have called for a reliable phylogenetic hypothesis of skates [ 10 ], the monophyly within these two (and further) rajid genera has not yet been examined comprehensively, neither morphologically nor genetically. Several studies from different fields of research have focused on a single species, particularly the model organism L. erinacea (Mitchill, 1825) [ 11 , 12 , 13 , 14 ], as well as L. naevus (Müller and Henle, 1841) [ 15 ]. Phylogenetic studies examining Leucoraja or Rajella species include those by McEachran and Dunn [ 8 ], Turan [ 16 ], Aschliman et al [ 17 ], Naylor et al [ 18 , 19 ], Chiquillo et al [ 20 ], and Lynghammar et al [ 21 ].…”

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catsharkScyliorhinus caniculareveal the molecular bases of sensory organ evolution in jawed vertebrates

“…Maximum chromosome size as described in GenBank. Reference publications [1] (Read et al 2017), [2] ( Zhang et al 2020), [3] (Sendell-Price et al 2023), [4] (Wagner et al 2023), [5] (Marra et al 2019), [6] this work, [7] (Yoo et al 2022;Marlétaz et al 2023), [8] (Venkatesh et al 2007;Venkatesh et al 2014). This work aims at filling this gap, focusing on sensory systems and using the small-spotted catshark Scyliorhinus canicula, an emerging model organism, as the reference species.…”