Transcriptomic Analysis of Somatic In Situ Regeneration in Green Macroalga Ulva prolifera (Ulvophyceae, Chlorophyta)

Somatic in situ regeneration (SISR) is a unique reproductive mode of the green-tide-forming alga Ulva prolifera. Based on reproductive and developmental characteristics, a previous study has speculated that SISR represents an early evolutionary form of somatic embryogenesis (SE) in land plants, but molecular evidence was lacking. In this study, time-series RNA-Seq was conducted during SISR, focusing on key regulatory modules in SE, including phytohormones, stress responses, epigenetic modifications, and transcription factors (TFs). Additionally, transcriptome data were subjected to homology analysis with 13 phylogenetically representative plant genomes. Results indicated that overall transcriptional dynamics during SISR were highly similar to those in SE, suggesting that the initiation of SISR likewise requires rapid auxin accumulation and transport, as well as the involvement of numerous stress-responsive genes. Epigenetic modifications displayed a sequential trend of dedifferentiation followed by redifferentiation. Notably, most key SE-related TFs were detectable among the differentially expressed genes (DEGs), and exhibited conserved regulatory relationships as in SE. Combined with the revealed homology of module-related genes between SISR and SE, these findings suggested that SISR and SE might share deep homology in terms of conserved molecular modules and utilize a similar core hierarchical regulatory network. This raised the possibility that the underlying molecular modules of SE could have evolved prior to plant terrestrialization.