Description
A plastid gene resource for algal evolution and metagenomics.
Algae are responsible for nearly half of global primary production and oxygen production. The plastid genome, a reduced descendant of an ancient cyanobacterial endosymbiont, is a central resource for studying their evolution and diversity. Thousands of algal plastid genomes have been sequenced, but their genes sit in separate records and are not organised by evolutionary relationship. ChlORIS (Chloroplast Orthologs Resource and Identification Suite) groups the plastid-encoded proteins of all algal phyla into orthologous gene families and makes them available for evolutionary and metagenomic research.
What ChlORIS contains
Section titled “What ChlORIS contains”ChlORIS is built from 2,254 publicly available algal plastid genomes, reduced to a non-redundant set of representatives and clustered into orthologous gene families. From these we kept 496 families with consistent gene names, and selected 224 well-represented core proteins that are shown in detail on the site. For these we provide:
- profile hidden Markov models (HMMs) with calibrated score cutoffs, for detecting plastid genes in new data;
- multiple sequence alignments for each gene family;
- predicted protein structures (AlphaFold 3);
- Pfam domain annotations, with each protein cross-linked to UniProt and InterPro;
- a plastid phylogeny of 857 algal taxa plus one land-plant reference, spanning all major lineages;
- a metagenomic reference database for assessing the quality of plastid metagenome-assembled genomes.
The Species page lists the source genomes, the Proteins pages show each core protein with its alignment and structure, and the Download page provides all resources in bulk.
What you can do with it
Section titled “What you can do with it”You can use ChlORIS for:
- phylogenetics: extracting conserved marker genes from plastid genomes to build trees;
- metagenomics: detecting plastid sequences in environmental data and estimating the completeness and contamination of plastid metagenome-assembled genomes;
- functional annotation: assigning Pfam domains and predicted structures to plastid genes;
- molecular evolution: using the alignments, structures and phylogeny in studies of selection, substitution rates and divergence times;
- DNA (meta-)barcoding: designing markers from the alignments for reference-based profiling of algae in environmental data;
- anything you want that we haven’t thought of: ChlORIS is CC0 licensed, so it can be used without restriction (with the exception of the protein structures, which are subject to the AlphaFold 3 terms of use).
Who are we?
Section titled “Who are we?”
PhD candidate working in bioinformatics and computational biology, applying these techniques in multi-omic contexts and exploring deep-learning methods to mine unknown marine algae.
Works at the interface of microbial ecology, evolution and bioinformatics. After a PhD on the microbiome of coral skeletons, she developed analytical tools to study human pathogens within microbiomes.
Senior Research Data Specialist at the Melbourne Data Analytics Platform, collaborating with researchers across the University of Melbourne on data-intensive research projects.
Interests span algal evolution, microbial symbiosis, genome biology and bioinformatics, with a fondness for computational simulation as a tool to explore ideas and methods.