Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e–4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.

作为不同生态系统中不可或缺的初级生产者，可以挖掘微藻基因组以获得生态洞察力，但许多门缺乏代表性的基因组序列。我们对来自不同地理和气候的 11 种不同门的 107 种微藻进行了培养和测序。该集合用于解决咸水和淡水微藻之间的基因组差异。淡水物种在核和核膜功能方面表现出以领域为中心的本体论富集，而咸水物种则在细胞器和细胞膜功能方面富集。此外，海洋物种的基因组中包含明显更多的病毒家族（p = 8e-4）。来自氯病毒、球状病毒、潘多拉病毒、马赛病毒、图潘病毒的序列，和其他病毒被发现整合到来自海洋环境的藻类基因组中。发现这些病毒来源序列被表达并编码多种功能。总之，这项研究全面定义了微藻基因组中蛋白质编码和病毒元件的范围，并为藻类耐盐提出了统一的适应性策略。