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

Background 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. Results 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. Conclusions The near-T2T genome of C. bella is the highest degree of chromosomal fusion observed in echinoderms, which represents a key evolutionary innovation in echinoderms. Also our findings decipher the strategies of C. bella to cope with environmental fluctuations of coral reef (e.g., UV radiation, temperature shifts, and pathogen pressure).