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Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt,  Styela clava , is an important invasive species. We used the chromosomal‐level genome and transcriptome of  S .  clava  to explore its genomic‐ and molecular‐network‐based mechanisms of adaptation to environments. Compared with  Ciona intestinalis  type A ( C .  robusta ), the size of the  S .  clava  genome was expanded by 2‐fold, although the gene number was comparable. An increase in transposon number and variation in dominant types were identified as potential expansion mechanisms. In the  S .  clava  genome, the number of genes encoding the heat‐shock protein 70 family and members of the complement system was expanded significantly, and cold‐shock protein genes were transferred horizontally into the  S .  clava  genome from bacteria. The expanded gene families potentially play roles in the adaptation of  S .  clava  to its environments. The loss of key genes in the galactan synthesis pathway might explain the distinct tunic structure and hardness compared with the ascidian  Ciona  species. We demonstrated further that the integrated thyroid hormone pathway participated in the regulation of larval metamorphosis that provides  S .  clava  with two opportunities for adapting to their environment. Thus, our report of the chromosomal‐level leathery sea squirt genome provides a comprehensive genomic basis for the understanding of environmental adaptation in tunicates.

Genomic basis of environmental adaptation in the leathery sea squirt ( Styela clava )