Supplementary dataset for: Genome-wide signatures of adaptation to extreme environments in red algae

The high temperature, acidity, and heavy-metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. Understanding the origin and evolution of adaptations to these extreme environments has long intrigued scientists. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites (e.g., endolithic) worldwide for >1 billion years. These poly-extremophilic red algae are models for studying a wide range of topics in cell evolution. Here, we analyze chromosome-level assemblies from three Cyanidiophyceae species, the Cyanidiales Cyanidium caldarium 063 E5 and Cyanidiococcus yangmingshanensis 8.1.23 F7 and the Galdieriales Galdieria sulphuraria 108.79 E11, to gain insights into environmental adaptation. We find that horizontal gene transfer (HGT) has played a major role in this process, as has other mechanisms such as subtelomeric gene duplication (STGD) of functional genes and the elimination of canonical eukaryotic traits, including microRNA processing. These extremophilic adaptation strategies are shared by the two major orders, Cyanidiales and Galdieriales, but most of the specialized genes evolved independently in each lineage. Our findings provide significant and novel insights into Cyanidiophyceae adaptation to hot-spring environments and demonstrate how the genomic consequence of extremophilic adaptation varies among the taxa in different microhabitats. The latter result underlines the power of local selection to shape eukaryotic genomes that face vastly different stresses, although the cells may live in close proximity.