Fabien Burki

Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...

Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts Bodo is a cosmopolitan genus of free living bacterivorous single-celled flagellates in the class Kinetoplastea. Members of genus Bodo are considered the closest free-living relatives to the parasitic ...

A new preprint from us using a single-cell genome pipeline to investigate diversity of uncultured Bodo spp. flagellates.

We isolated 7 Bodo spp. cells from a single environmental sample and show that they represent 3 Bodo sp. each with a unique species of bacterial endosymbiont. #protistsonsky

From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding In the last decades, environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecol...

Researchers present the BaNaNA (Barcoding Nanopore Neat Annotator) pipeline and display the effectiveness of long-read Nanopore sequencing for protist biodiversity, ecology and evolution research.

🔗 doi.org/10.3897/mbmg...

@ankarn.bsky.social @fabnot.bsky.social

I wish these were my areas of expertise, look at this place

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

Our latest, led by Edu Ocaña-Pallarès and @ssolo.bsky.social, a timescale for fungal phylogeny that wrangles calibration from the unstructured fossil record of fungi and a history of horizontal gene transfers

www.nature.com/articles/s41...

Improving RNA-seq protocols www.biorxiv.org/content/10.1...

Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵

I've seen this several times: when Acantharians get big enough they like to eat tintinnids. And they always orient with the lorica opening pointed in: like they are slurping up a little jello shot. That glass house can't protect you from these weird predators little ciliate! 🦑 #protistsonsky

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae Nature Communications - Phaeocystales are ecologically significant nanoplankton whose evolutionary history and functional diversity remain incompletely characterized. Here, the authors integrate...

Study reveals the hidden genomic diversity & global distribution of Phaeocystales — bloom-forming algae with surprising mixotrophic strategies, viral integrations, & adaption to polar vs temperate zones. #protistsonsky
Big step forward for marine ecology & biogeochemical models. 🧬🌊
📖 rdcu.be/eI4nv

A New Age of Advanced Volume Microscopy for Protists onlinelibrary.wiley.com/doi/10.1111/... #protists #protistsonsky

Eukaryogenesis From FECA to LECA: Radical Steps Along the Way How did the last eukaryotic common ancestor (LECA) population evolve? Recent evidence shows an Asgard archaeon-like organism acquiring a bacterium, the future mitochondrion, going from symbiosis to e...

Eukaryogenesis From FECA to LECA: Radical Steps Along the Way onlinelibrary.wiley.com/doi/10.1002/...

Very true. The time it takes to gain energy back after teaching a class is often not properly factored in

#ProtistsOnSky
the elephant in the (protist)room...

I have thousands of #marineplankton microscopy images and measurements and would like to make these available to researchers. Where’s the best place to put them and how do scientists like their metadata? 🧪🦑

#protistsonsky

Evolutionary refinement of mitochondrial and plastid targeting sequences coincides with the late diversification of land plants Abstract. Plastids and mitochondria are key to plant survival and adaptation. The evolutionary progress of land plants (embryophytes) witnessed gene and ge

Evolutionary refinement of mitochondrial and plastid targeting sequences coincides with the late diversification of land plants academic.oup.com/mbe/article/...

Are you a recent PhD interested in a postdoc in Canada? Up to 20% of NSERC Postdoc Fellowships (70k/y for 2y) will be awarded to International applicants, who did their PhD outside of Canada. Deadline is 17 October. See: www.nserc-crsng.gc.ca/Students-Etu...

While it could have been a wild goose chase, finding this one is special to me because we were stacked against the odds

Comparative single-cell genomics of two uncultivated Naegleria species harboring Legionella cobionts journals.asm.org/doi/10.1128/... #protists #protistsonsky

Comparing the precision of two digital PCR applications for copy number comparisons in #protists www.nature.com/articles/s41... #protistsonsky

These are good changes, especially this: B1 <<should allow the panels to answer the question “is this a great idea that would be worth pursuing?”, while the question for>> B2 <<is “can that idea be pursued realistically, and if so, in the manner and with the approach that the applicant proposes?”>>

We have tried chemical fixation but this was not successful with these "bottle" cells, and we don't have easy access to cryo. @fmikus.bsky.social did plunge one of our cultures when we were at UBC, but I haven't heard how this went

Structure and function of a huge photosystem I–fucoxanthin chlorophyll supercomplex from a coccolithophore Photosystem I (PSI) is a pigment-protein complex, which converts light energy into chemical energy in photosynthesis. Among photosynthetic organisms, PSI-LHC (light-harvesting complex) structures exhi...

www.science.org/doi/10.1126/...
#protistsonsky

What’s the scale?

Expanding our Paulinella factory and hopefully more to come. @thealgaeman.bsky.social is the master grower, quite a tour de force for these very rare cells. @erc.europa.eu supported research

I broke some shells of Galeripora artocrea, to look at their algal hostages...and accidentally created Pac-Man amoebae. #amoebae #peatlands #ProtistsOnSky

Could you briefly explain why is eRNA in principle more contamination-prone than eDNA? Thank you

What you're looking at is a brand new protist species! 🤯🔬
Isn't it beautiful?
This image is just a glimpse of what's to come. We can't wait to share our full findings soon, in partnership with Guifré @beaplab.bsky.social @luisjagago.bsky.social. Stay tuned! #NewSpecies #protistsonSky #diversity

#protistsonsky

#protistsonsky