SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The SAR11 clade, also known as the order Pelagibacterales, is among the most abundant bacterial lineages in the ocean and plays central roles in marine biogeochemical cycles. However, many SAR11 genes remain functionally uncharacterized, highlighting the need for a comprehensive, integrated catalog that supports genomic, functional, and ecological analyses across the clade. Here, we present the SAR11 Genome Atlas, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information. To demonstrate its utility, we used environmental expression profiles to identify OGs associated with high-latitude environments, recovering OGs known to be involved in cold adaptation and proposing a functional hypothesis for an uncharacterized protein. We further analyzed phylogenetic distribution patterns to identify mutually exclusive functional modules, including candidate alternative systems for Mn/Zn homeostasis and phosphate acquisition, and to examine their association with distinct oceanographic environments. Together, these case studies highlight the value of the SAR11 Genome Atlas for generating ecological hypotheses by providing environmental and phylogenetic context for genes of interest. Through a user-friendly web interface, the SAR11 Genome Atlas enables researchers to explore genomic, environmental, and structural information without specialized computational expertise. All data and analysis outputs are freely accessible online at [https://stsnsn.github.io/SAR11_Atlas/].