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 functiona..., Whole genome sequencing (WGS) and whole transcriptome sequencing (WTS). For genome and transcriptome sequencing, both short-read and long-read sequencing were conducted. For PacBio whole genome sequencing (WGS), we used SMRTbell® Express Template Prep Kit 2.0 (Pacific Biosciences) with a 15 kbp size selection to construct Sequel I sequencing libraries of Cyanidium and Cyanidiococcus. For Galdieria PacBio WGS, SMRTbell® Express Template Prep Kit 1.0 (Pacific Biosciences) with a 9 kbp size selection was used to prepare the RS II sequencing library and SMRTbell Express TPK 2.0 (Pacific Biosciences) was used for HiFi library preparation. All experiments followed the manufacturer's standard protocol, without shearing step in Cyanidium and Galdieria samples. SQK-LSK109 ligation kit (Oxford Nanopore Technologies) was used to construct a library of Galdieria PromethION sequencing without shearing step and a 20 kbp size selection. For Illumina HiSeq2500 WGS of Cyanidium and Galdieria species, Tr...,