ChlORIS: Chloroplast Orthologs Resource & Identification Suite

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/.