Lee Y et al. (2022), Chromosome-level genome assembly of Plazaster b...

ECB-ART-51031

Gigascience 2022 Jul 09;11. doi: 10.1093/gigascience/giac063.

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Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity.

Lee Y , Kim B , Jung J , Koh B , Jhang SY , Ban C , Chi WJ , Kim S , Yu J .

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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.

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	Figure 1:. (A) Adult Plazaster borealis. Photograph by National Institute of Biological Resources [77]. (B) Sampling spot of P. borealis studied in this research.
	Figure 2:. A phylogenetic tree of P. borealis and 6 other species. This tree was constructed using protein sequences of 7 species, showing gene family expansion and contraction. The number below the branches represents the number of gene families with either expansion (blue) or contraction (red). The ratio of expanded and contracted gene families is expressed in the pie chart above the branches. The numbers at the node indicate the bootstrap value. The species used in the tree are P. borealis, A. rubens, A. planci, P. miniata, L. variegatus, P. parvimensis, and S. purpuratus.
	Figure 3:. Syntenic relationship of P. borealis and species of the order Forcipulatida. (A) Synteny between A. rubens and P. borealis. The syntenic blocks were calculated with MCscan. (B–D) Syntenic relationship of P. borealis between A. rubens (B), Pisaster ochraceus (C), and Marthasterias glacialis (D). Genomic sequences were compared with Chromeister based on inexact k-mer matching.
	Figure 4:. GO enrichment analysis of expanded gene families of P. borealis.
	Figure 5:. Results of GO enrichment analysis of positively selected genes. BP, GO Term Biological Process (green); CC, GO Term Cellular Component (red); KEGG (blue).