Francois Sabot
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francoissabot.bsky.social
Francois Sabot
@francoissabot.bsky.social
400 followers 510 following 650 posts
Scientist, biologist, #evolution and #pangenomics, #bioinformatics, #AI and #OpenScience @ird_fr - and a little bit a #geek too
mastodon: @francois_sabot@genomic.social
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francoissabot.bsky.social
Animals are just a few part... from the same location
Visualizing biomass on earth, not only animals but all kingdoms. Mostly plants, then bacteria, fungi, archae, protists, animals, then viruses. Humans are less than 0.01% of the total biomass...
November 12, 2025 at 9:34 AM
francoissabot.bsky.social
Nina compared it to state-of-the-art tools for genome-to-genome transfer (LiftOff), genome-to-graph (VG and ODGI), and GrAnnoT is more conservative and fast, and is the only tool able to go efficiently from genome-to-graph AND from graph-to-genome!
Genome to genome transfer comparison. GrAnnoT and Liftoff run time for 1-12 transfers were measured using the command /usr/bin/time. Liftoff was run both in GFF and DB mode. GrAnnoT values are presented including or not the graph building time.
October 30, 2025 at 3:46 PM
francoissabot.bsky.social
Basically, it converts/transfers coordinates from any embedded genome in the graph to the graph, and from the graph to any other embedded genome! It can transfer with a certain level (user defined) of identity/length, and provide alignments between source and target.
GrAnnoT overview. Step 1: the position of the feature is projected from the source genome to the graph using the positions of the nodes on the source genome. Step 2: the position of the feature is projected from the graph to the target genome (a). The first and last nodes from the feature that are on the target genome (the blue ones) are the ends of the feature in this genome, and everything in between is considered as part of the feature. The differences between the two genomes in this region in terms of path in the graph mirror the differences between the two versions of the feature. If these differences are too important and the transfer does not reach the coverage and/or sequence identity thresholds, the annotation is not transferred (b).
October 30, 2025 at 3:46 PM
francoissabot.bsky.social
Finally, B. prasinos is also known to have a very strange SOC (small outlier chromosome, the 19th), supposedly linked to viral resistance. Using our high quality assemblies, we found some shared sequences at an unexepected length !
Chromosome 19 SOC shared sequences between B. prasinos strains. Chord plot representation of chromosome 19 shared sequences between strains of the geographically close water basins (Left) and between all 24 B. prasinos sequenced strains (Right). Chromosome color corresponds to basin and geographical distribution of strains as shown in Figure 5 : Blue, Arctic ocean ; Green, North sea and English channel ; Red, Mediterranean sea. Only shared sequences longer than 500 bp are displayed.
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
B. prasinos possesses two haplotypes on its "BOC" (Big outlier Chromosome), haplotypes shared between many strains and almost with no variation within. The ratio between the two is basin dependent
Phylogenomic of B. prasinos linked to strain origin and Chromosome 14 BOC haplotypes. (Left) Maximum-likelihood phylogenetic tree of B. prasinos strains based on 1,200 shared genes. (Right) Maximum-likelihood phylogenetic tree of Bathycoccus strains based on 69 shared genes located on chromosome 14. Only branches with bootstrap values higher than 90% are displayed. Gene concordance factors are displayed for all visible branches. Genomic diversity and haplotypes biogeography of Bathycoccus prasinos big outlier chromosome. (A) Alignment of Chromosome 14 from B. prasinos strains RCC4222 and A8. Colors indicate syntenic regions and structural rearrangements. Y axis displays the GC content of the corresponding sequences. (B) Divergences between local single nucleotide polymorphism (SNP) density and genome wide SNP density along a 20 kb sliding window. (C) Divergences between local structural variation (SV) density and genome wide SV density along a 20 kb sliding window. SNP and SV calling was computed for each BOC haplotype against strain RCC4222 for BOC A and strain A8 for BOC B. Characterization of BOC haplotype geographical distribution. (A) BOC haplotypes ratio based on read mapping from TARA ocean metagenomic datasets in stations with B. prasinos relative abundance > 0.1%. (B) BOC haplotype ratio among strains isolated in the Banyuls Bay (Left)(n=55) and the Baffin Sea (Right)(n=183).
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
MAG are really valuable in algae (meta)genomics for species discovery. However, they are not suitable for intraspecific variations: chimerical contigs, fragmented and partial genomes, and so on.
Qualitative comparison between de novo genome assembly from whole-genome sequencing data (WGS) and metagenome assembled genomes (MAGs) of Bathycoccus prasinos. (A) Maximum-likelihood phylogenetic tree of B. prasinos available genomes based on 265 shared genes. Only branches with bootstrap values higher than 90% are displayed. Gene concordance factors are displayed for all visible branches. (B to E) Distribution of principal assembly statistics between available MAGs (n=11) and whole genome assemblies produced from isolated strains of B. prasinos (n=24). Median values are displayed for reference.
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
Surprise ! Using phylogenomics we identified/confirmed the presence of a third species, Bathycoccus catiminus! It was previously supposed to be a subgroup in the prasinos species (B3 type), but is in fact a single species!
Phylogenomic of the Bathycoccus genus and B. catiminus characterization. (A) Maximum-likelihood phylogenetic tree of Bathycoccus strains based on 1,200 shared genes. Species separation is derived from the branch length and marked by colors. The tree includes strain UST710 isolated and sequenced by Xu et al. (2024) for reference. O. tauri and M. pusilla are used as outgroups. Only branches with bootstrap values higher than 90% are displayed. Gene concordance factors are displayed for all visible branches. Transmission electron microscopy images of (B) B. prasinos, (C) B. catiminus strain isolated from the Banyuls bay, and (D) a close up of detached spider web scales from B. catiminus. N: nucleus, Cp: chloroplast, St: starch granule, Sc: scales. Bar = 100 nm. (E) Presence of B. catiminus in Banyuls bay seawater samples from 2019-2020 and 2020-2021 phytoplanktons blooms, identified using specific primers designed from non-conserved sequences of TOC1 ORF specific to B. catiminus. Fig S1: (A) Maximum-likelihood phylogeny and (B) 2D centroid structure of available Bathycoccus 18S rRNA ITS2 region. Only bootstrap values higher than 90% are displayed. Notable structural variations compared to B. prasinos 18S ITS2 region are marked by arrow and circles. 18S sequences were obtained from B. prasinos RCC1105 reference strain, B. calidus RCC716 strain and Bathycoccus sp. G8 strain respectively. Bathycoccus Kara environmental sequence was obtained from Belevich et al. (2021).
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
The assemblies were of very high quality, almost complete, and better than the published reference genome.
Genome assemblies statistics and quality assessment. (A) BUSCO completion score of genome assemblies for the 28 de novo assembled Bathycoccus genomes using the chlorophyta_odb10 library. RCC1105 corresponds to the reference genome produced by Moreau et al. (2012), while RCC4222 corresponds to the de novo assembly obtained from a clonal strain of RCC1105. (B) PHRED quality score of genome assemblies per chromosome. (C) Distribution of principal assembly statistics. The N50 corresponds to the sequence length of the shortest contig at 50% of the total assembly length. (D) Comparison of BUSCO single-copy completion score using complete genome sequence or annotated CDS sequences as input.
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
From a large sampling we obtained 28 high quality genomes for the species
Sampling, sequencing, genome assembly and annotation strategy of Bathycoccus. (A) Geographical distribution of the sampling sites for the selected Bathycoccus strains. The number of strains sampled at each site is indicated. Colors correspond to the oceanic basin of origin: blue, Arctic Ocean; green, Atlantic Ocean; red, Mediterranean Sea; grey, Indian Ocean. (B) Summary of the sequencing, assembly and annotation strategy.
October 30, 2025 at 3:39 PM
francoissabot.bsky.social
No comment...
October 14, 2025 at 1:37 PM
francoissabot.bsky.social
A l'inauguration du Cluster PostGenAI de SCAI @sorbonne-universite.fr pour l' @ird-fr.bsky.social . L'IA est à la fois une chance pour le développement mais aussi un objet de recherche, à étudier et à utiliser (dans la mesure de l'éthique sociale et environnementale) #AI
Salle des Cordeliers à Paris, avec des fenêtres en ogive
April 1, 2025 at 4:13 PM
francoissabot.bsky.social
And it is much faster than the state-of-the-art tool for linear transfer LiftOff

4/5
Transfer rate comparison between liftoff and grannot on 1 to 12 genome of rices. Grannot is much faster
March 3, 2025 at 9:51 AM
francoissabot.bsky.social
GrAnnoT is fast, relies on the graph structure itself, and ensures a biologically relevant transfer of annotation: the frameshift rate induced by the annotation transfer is significantly lower in CDS

3/5
the frameshift rate induced by the annotation transfer is significantly lower in CDS
March 3, 2025 at 9:51 AM
francoissabot.bsky.social
to the graph itself or to any of the embedded genome within!

2/5
The picture despites the different steps in GrAnnot: step 1: transfer of the annotation from the source genome to the graph. Step 2 , the transfer from the graph to any target genome
March 3, 2025 at 9:51 AM
francoissabot.bsky.social
@murielgrosb.bsky.social is presenting her HDR docentship right now ! @ird-fr.bsky.social #palms #datepalm
February 7, 2025 at 1:10 PM
francoissabot.bsky.social
I am attendant the Software Heritage 2025 Symposium at @unesconow.bsky.social for #opensoftware #swh2025
Unesco amphitheatrum People are Washington for beginning
January 29, 2025 at 1:11 PM
francoissabot.bsky.social
According to Dall-E, here is my office: #bioinformatics #pangenomics #ttrpg #cats
December 18, 2024 at 3:19 PM
francoissabot.bsky.social
Formation sur les logiciels libres #opensource aux services de valorisation de l' @ird-fr.bsky.social ce matin!
Training on #OpenSoftware for valorisation services this morning
December 18, 2024 at 8:44 AM
francoissabot.bsky.social
Aujourd'hui au Cap commence le colloque #ScienceOuverte au Sud avec un focus sur les aspects de l'édition scientifique @ird-fr.bsky.social

Today in Cape Town started the #OpenScience in the South with a focus on scientific edition

#inclusion #equity #équité
December 9, 2024 at 10:12 AM
francoissabot.bsky.social
Our Colleague Nora Scarcelli is currently presenting to a non-scientific audience the #genetic #vulnerability concept, applied to African Yam 🧬 🧪 💻
Dr Nora Scarcelli presenting the concept of genetic vulnerability
November 26, 2024 at 1:12 PM
francoissabot.bsky.social
Age yourself with your first computer

Amstrad 464 a cassette audio.... enregistrement au bouton record
November 24, 2024 at 10:23 AM
francoissabot.bsky.social
Aujourd'hui rencontre des membres de l'ESR avec Gitlab au Lieu de la Transformation! Au menu #opensource, software et hackathon @ouvrirlascience @ird_fr
November 25, 2024 at 4:23 PM
francoissabot.bsky.social
Almost finished with out training on @nanopore with the @MRiseproject project... very nice team and trainees!
November 25, 2024 at 4:22 PM
francoissabot.bsky.social
This week we are in Argentina with @JulieOrjuela and colleagues for @nanopore training in lab and #bioinformatics
Thanks @IFB_Bioinfo for the VM support ! @ird_fr @ItropBioinfo @LabDiade
November 25, 2024 at 4:22 PM
francoissabot.bsky.social
From Quito @JulieOrjuela and Marie are presenting basics on reads N50 for our @nanopore teaching @AGaelBilhaut @ird_fr @ItropBioinfo @IFB_Bioinfo
November 25, 2024 at 4:22 PM