Chromosome-level genome assembly ofPlazaster borealissheds light on the morphogenesis of multiarmed starfish and its regenerative capacity

Abstract

Background Plazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology. Findings In total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration. Conclusion This first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.

A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis)

“…The chromosome number is consistent with previous karyotyping studies on some asteroids, including species from Forcipulatida 53 . This is also proved by recent genome studies on several starfish species where 22 pseudo-chromosomes were identified by the Hi-C method 22 – 24 .…”

“…cf. ophiactis genome assembly is much larger than genomes reported for other asteroids, including species in the order Forcipulatida (402–561 Mb) 21 – 24 , and those in the other order, Valvatida (384–608 Mb) 20 , 25 , 52 . In addition, 22 pseudo-chromosomes were generated for the Z .…”

“…cf. ophiactis and the other two Forcipulatida star fish, Asterias rubens (GCF_902459465.1) 56 and Plazaster borealis (GCA_021014325.1) 24 were inferred and visualization by Blastp and NGenomeSyn v1.37 57 . The three starfish appeared to have very conserved syntenic relationships as every chromosome matched each other well (Fig.…”

The brittle star genome illuminates the genetic basis of animal appendage regeneration

“…For the sea urchin P. lividus and the black sea cucumber H. leucospilota , we used previously reported gene annotations (Chen et al 2023; Marlétaz et al 2023). We generated a draft homology-based annotation for the spiny sea star M. glacialis (Lawniczak et al 2021) with MetaEuk (Levy Karin et al 2020) using proteins of the sea urchin S. purpuratus (Spur_5.0, available in Ensembl Metazoa v56, (Sea Urchin Genome Sequencing Consortium et al 2006)), the crown-of-thorns sea star A. planci (OKI_Apl_1.0, available in Ensembl Metazoa v56 (Baughman et al 2014)) and the octopus sea star P. borealis (Lee et al 2022). One-to-one orthologous genes were identified by reciprocal best blast hit between pairs of compared genomes, using diamond (Buchfink et al 2021).…”

Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis

“…The longest protein sequences of A. amurensis and other five asteroid species including Acanthaster sp . 63 , Asterias rubens 64 , Patiria miniata 65 , Plazaster borealis 66 , and Zoroaster cf. ophiactis 67 were utilized to identify orthologous groups using OrthoFinder (v2.5.5) 68 with the parameters ‘-S diamond’, and the sea urchin Lytechinus variegatus 69 was selected as an outgroup.…”