The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment

Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal’s adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2 ; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP ; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2 ; and Ribosomal RNA Processing 9, RRP9 ) were subject to positive selection in the genome of C. heheva , which contributes to their adaptation to hypoxic environments. The genome sequence of the deep-sea echinoderm Chiridota heheva and comparative analyses identify genes that are suggested to be associated with deep-sea adaptation.