The near-T2T genome of the feather star Cenometra bella suggests potential evolutionary innovations and coral reef habitat tolerance

Crinoids are highly conservative echinoderms, retaining ancient features since the early Ordovician, making them classic “living fossils” invaluable for studying evolution and biodiversity. Their evolutionary stability is marked by minimal morphological changes, a sessile lifestyle, and exceptionally slow evolutionary rates, rendering them unique among marine groups. However, they have long lacked high-quality genomic resources, hindering insights into the genomic evolution of early echinoderm lineages. Here, we present the first near-telomere-to-telomere (T2T) genome assembly (354.7 Mb, 12 chromosomes, GCI score = 75.0837) of the coral reef-dwelling feather star Cenometra bella using PacBio HiFi and Hi-C technologies. The assembly exhibits exceptional continuity (contig N50 = 28.25 Mb) and completeness (97.5% BUSCO genes), surpassing existing crinoid genomes. Precise identification of telomeric repeats and centromeric regions revealed critical genes associated with intracellular metabolism, signal transduction, and nervous system regulation. Macrosynteny analyses uncovered nine chromosomal fusion events, reducing the presumed 23 ancestral echinoderm linkage groups to 12 chromosomes. Genes on fused chromosomes were functionally enriched in attachment-related processes (e.g., cell adhesion), energy metabolism, environmental sensing, and immune response. Furthermore, expanded gene families (28 families, 455 genes) and positively selected genes (194 genes) were linked to lipid synthesis, DNA repair, and membrane stability. The near-T2T genome of C. bella is the highest degree of chromosomal fusion observed in echinoderms, which may represent a potential evolutionary innovation within this phylum. Furthermore, our comparative genomic results suggest potential adaptive strategies enabling C. bella to tolerate fluctuating coral reef conditions, including ultraviolet radiation, thermal variation, and pathogen stress.