The SAR11 Genome Atlas is presented, 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.
Abstract
The SAR11 clade, also known as the order Candidatus 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 hypothesis for the function of 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 associate these modules with distinct oceanographic environments. Together, these case studies demonstrate that the SAR11 Genome Atlas supports complementary analyses that connect environmental signals to genes of interest and use phylogenetic or functional distributions to generate hypotheses about ecological specialization. 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/]. The SAR11 Genome Atlas thus provides a scalable framework for generating and testing hypotheses that connect SAR11 genomic variation to protein function and oceanographic context, supporting advances in marine microbial ecology and biogeochemistry.
Chloroplast or plastid genomes are essential resources for studying the evolution and diversity of algae and land plants. Although thousands of plastid genomes have been sequenced, their full potential has not been realised; derived resources such as orthogroup databases and reference datasets for metagenomic profiling remain underdeveloped. We present the ChlORIS database to address these problems across all algal phyla. From 2,254 publicly available algal plastid genomes, after dereplication we clustered 2,531 orthogroups from the annotated proteins and selected 496 orthogroups with consistent gene naming, enabling cross-genome comparisons of homologous plastid proteins. We further selected 224 core orthogroups, each containing more than 10 protein sequences, for which we produced score-calibrated hidden Markov models (HMMs), multiple sequence alignments and predicted protein structures. The value of these resources for phylogenomics is demonstrated through a large-scale plastid phylogeny of 859 taxa spanning all major algal lineages. We characterised the protein HMMs by cross-referencing them to Pfam domains and calibrated score cutoffs for reliable detection. The metagenomic database, HMM library, nucleotide and amino acid alignments, predicted structures and protein metadata, cross-linked to UniProt and InterPro (Pfam), are openly available on the ChlORIS website at https://chloris.codeberg.page/.
Yuhao Tong, Vanessa Rossetto Marcelino, Robert Turnbull et al.· bioRxiv· 0 citations
The GenomeCompendium is released, a public database and interactive analysis tool for complete prokaryotic genomes and it is shown that complex, repeat-rich genomes are more common than previously estimated.
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Kathryn Kananen, Nghi Tran, Patrick H. Bradley· bioRxiv· 0 citations
A pan-genome of 17 Nannochloropsis species comprising 14,851 gene families is constructed and a distinct genetic architecture for lipid metabolism is defined: Gene families associated with vesicular transport formed a conserved core functional module, whereas the genetic collection for lipid metabolism showed greater plasticity and was primarily classified as part of the soft-core genome.
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