Dynamic changes in gene expression in regeneration of Halisarca dujardinii (Porifera, Demospongiae)

Sponges occupy a key position at the base of the phylogenetic tree. Their regenerative abilities are extremely broad and their reparative morphogenesis is diverse. We performed RNA-seq at different stages of regeneration in the marine sponge Halisarca dujardinii (Demospongiae) to assess gene expression changes after body fragment removal. A small (no more than 5%) body fragment was removed under a stereomicroscope, then sponges on substrate were cultured in a seawater aquarium at 12 degrees Celsius. At intervals (30 min, 1, 3, 6, 12, 24 h), tissue adjacent to the wound was dissected out and immediately frozen in liquid nitrogen. Only tissues immediately adjacent to the wound were used for RNA isolation to level out the influence of tissues not involved in regeneration on DE analysis. Intact sponges were used as controls. All experiments were performed in three biological replicates. RNA was isolated using Lumisol (Lumiprobe, cat. no. 91415) and purified using spin columns (Evrogen, cat. no. BC033).