Ore Francis

Check out our new paper on adopting a trait-based framework for protist diversity! We make the case for a unified protist trait database, how to build it, and how it could transform research on protist ecology and evolution.
#protistsonsky

Allostery is a widespread cause of loss-of-function variant pathogenicity Allosteric communication between non-contacting sites in proteins plays a fundamental role in biological regulation and drug action. While allosteric gain-of-function variants are known drivers of onc...

New preprint: Allostery is a widespread cause of loss-of-function variant pathogenicity by the great
@xt117.bsky.social
biorxiv.org/content/10.1...

Direct link to handbook: zenodo.org/records/1569...

Modern microbialites harbor an undescribed diversity of chromerid algae Chromerid algae and the heterotrophic colpodellids together make up the chrompodellids, which are the closest known relatives to apicomplexan parasites [1]. As apicomplexans are prolific parasites of ...

New ‪preprint! Through plastid MAGs and 18S rRNA gene retrieval 🧬 we identify chromerids (including a novel clade ⭐) associated with marine and freshwater microbialites across the globe 🌎, expanding their ecological niche beyond coral reefs 🪸. #ProtistsOnSky #MicroSky #Algae

Proud to have authored this review with brilliant people. Hope we inspire more attempts to sequence the #protist genomes that are within reach! Huge thanks to Alexandra Schoenle for leading. #ProtistsOnSky
authors.elsevier.com/sd/article/S...

Global Metagenomics Reveals Hidden Protist Diversity Protists, defined as unicellular eukaryotes distinct from animals, plants, and fungi, are a polyphyletic group that predominates the eukaryotic tree of life, exhibiting significant phylogenetic diversity and fulfilling critical ecological roles. Historically, research has prioritized protists associated with animals and plants, particularly those of medical significance, thereby overlooking the majority of protist diversity. Conventional molecular methods, such as 18S rRNA gene amplicon sequencing, frequently encounter limitations, including primer binding bias and PCR bias caused by gene length variations, creating a biased perspective of understudied protistan diversity. Further, most protist lineages are notoriously difficult to cultivate. Here, we apply a cultivation-independent approach in which we analyzed over 27,000 assembled metagenomes and protist single cell genomes and 21 long 18S rRNA gene amplicon data sets from various global ecosystems, including marine, freshwater, and soil environments. We recovered 157,958 18S rRNA gene sequences (≥800 bp), which clustered into 103,338 operational taxonomic units (OTUs) at 97% sequence identity and 24,438 OTUs at 85% identity. Notably, 69% of 13,238 non-singleton clusters at 85% identity consisted exclusively of environmental sequences, uncovering a wealth of yet uncultivated and unclassified novel protist diversity. A comprehensive taxonomic framework of eukaryotes based on concatenated 18S and 28S rRNA genes that incorporated most novel lineages revealed substantial underrepresentation of Amoebozoa, Discoba, and Rhizaria in reference databases, with many lacking isolate or genome sequence representation. Further, we identified 13 eukaryotic lineages with novelty on higher taxonomic ranks, such as class and phylum-level, that lack representation in public databases. The corresponding 85% OTUs were primarily affiliated with Excavata, with some branching closely to the root of the eukaryotic tree. Comprehensive analysis of the global distribution of eukaryotes revealed uneven microbial eukaryotic diversity across supergroups and ecosystems, with notable novelty particularly in soil and marine environments. We then examined co-occurrence between protists and prokaryotes, predicting putative symbiotic or predator-prey relationships, particularly among understudied protist groups with bacteria such as Verrucomicrobia and Rickettsiales. Our results substantially enhance the understanding of protistan diversity and distribution, revealing taxonomic blind spots and laying groundwork for future studies of these organisms' ecological roles. ### Competing Interest Statement The authors have declared no competing interest.

Global Metagenomics Reveals Hidden Protist Diversity | bioRxiv https://www.biorxiv.org/content/10.1101/2025.03.26.645542v1

Our paper on myxozoan genomes is out now in G3! See thread below for a brief recap (slight change of title from the preprint, same content).

Thank you also to @arunsethuraman.bsky.social for handling the manuscript and @joannamasel.bsky.social for helpful comments.

academic.oup.com/g3journal/ad...

Genomics career profile: Postdoctoral Research Scientist (Ecology) at Wellcome Sanger Institute In this career profile, Katie describes her role as a Postdoctoral Research Scientist working in ecology. This is one of a series of career profiles exploring lots of different jobs in genomics.

Start celebrating our women in science and inspire the next generation. What better way than to show relatable individuals.
#WomenInScience #ChatBiology #CelebrateWomenNow #InspireTheNextGeneration

www.yourgenome.org/theme/my-car...

www.yourgenome.org/theme/career...

@engagewcs.bsky.social

I'll be talking about my #ProcB isopod phylogenomics paper in the Royal Society Publishing Ecology & Evolution Online Seminar Series, live (with Q&A) next Weds 26th Feb 2pm (UK).
Please reshare to reach all the lovers of #isopods (& #phylogenomics), who might be interested in their #evolution!
🧪