Kuba Sawicki

Epitranscriptomic and expression profiling in Riccia fluitans across diverse environmental conditions Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), are critical regulators of pl…

Our latest study reveals how RNA modifications (m⁶A, m⁵C, and pseudouridine) shape the environmental adaptation of the amphibious liverwort Riccia fluitans. 🌿💧
Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome.
#UMW #Riccia
📄 Read here: www.sciencedirect.com/science/arti...

NEW ARTICLE FROM THE LAB 🎉🍀🧫

Groundbreaking work performed by @hueihsuantsai.bsky.social and all!

Please, go have a read! Congrats to making it to the cover!!!

www.science.org/doi/10.1126/...

TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing AbstractMotivation. Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of t

We just published TAILcaller 🧬 — an R package for analyzing poly(A) tail length directly from @nanoporetech.com Dorado BAMs.
✅ Works with dRNA & cDNA
✅ PCA, volcano/MA plots, heatmaps
✅ Adaptive tests beyond Wilcoxon

Case studies: 🌱 Riccia fluitans
#liverworts #UWM

academic.oup.com/bioinformati...

Taxonomic and functional differentiation of soil and thallus microbiomes in Riccia sorocarpa - Biologia Liverworts, as early-diverging land plants, host unique and ecologically important microbiomes, yet remain largely understudied in microbial ecology. In this study, we investigated the taxonomic and functional composition of microbial communities associated with Riccia sorocarpa, focusing on the thallus and adjacent rhizosphere soil. Using nanopore sequencing and metagenomic analysis, we reveal a significantly higher microbial diversity and functional specialization in the thallus microbiome compared to soil. Despite a shared core microbiota, specific bacterial and fungal taxa are selectively enriched in the thallus, likely driven by host-derived factors. Functional profiling highlights an overrepresentation of nitrogen and sulfur cycling, phototrophy, and plant-associated pathways in the thallus, whereas soil communities are dominated by heterotrophic decomposition processes. These findings support the concept of R. sorocarpa as a holobiont and emphasize the ecological and biotechnological potential of liverwort-associated microbiomes. Our results provide new insights into plant-microbe interactions in early land plants and their roles in ecosystem function and resilience.

Our new study on the liverwort Riccia sorocarpa reveals its thallus is a microbial biodiversity hotspot. We found a significantly richer and more functionally specialized microbiome on the plant compared to the surrounding soil.

Read more:

doi.org/10.1007/s117...

#Microbiome #Liverworts #UWM

We're diving deep into the world of plant biology by studying the liverwort Apopellia endiviifolia.

Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics.

#Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts

RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU) - BMC Bioinformatics Background Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal,...

Excited to share our new paper in BMC Bioinformatics! We present RSCUcaller, a user-friendly R package to analyze synonymous codon usage bias. It's a versatile tool for genomics & molecular biology research. #RStats #Bioinformatics #CodonUsage bmcbioinformatics.biomedcentral.com/articles/10....

Got a chance to take the @nanoporetech.com hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉

(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)

New paper in Cladistics explores the tricky phylogeny of feather grasses (Stipeae) using mitochondrial genomes.The study features the first fully assembled mitogenome in the tribe using @nanoporetech.com sequencing:
#Botany #UWM
onlinelibrary.wiley.com/doi/10.1111/...

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha liverworts and interrogate the mechanisms enabling virulence in non-flowering and flowering plants. Their resu...

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants

Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.

Out now in Current Biology: www.cell.com/current-biol...

Engineering resistance with help from Liverworts, Mosses and Ferns | John Innes Centre Plant diversity and synthetic biology offer solutions to the global challenge of crop protection Non-flowering plants such as liverworts, mosses, and ferns belong to divergent lineages with ancient…

Engineering resistance with help from Liverworts, Mosses and Ferns

@Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...

HTL pippetes arę bulletproof.

Yes, but it's going slow, I mean translocation speed is much lower than DNA. I think we'll not achive 20Gbp from single FC. Anyway, in the case of RNA002 5-6Gbp was the best we could get.

The first run of @nanoporetech.com RNA004 in our lab. Big leap forward in quality and output. The times like this I wish we have Promethion24 and run all 8 flow cells in parallel.
#liverworts #epitranscriptomics #Apopellia

Elsevier’s stranglehold on academia: How publishers get rich off our data Academic publishers’ most valuable asset used to be their journals. Now, it’s the data they collect from researchers and then sell. That is extremely concerning, a growing group of Groningen researche...

Elsevier products: ScienceDirect, Scopus, Mendeley, SciVal, SSRN, Pure, Interfolio. . .and that's not all.

"They know what you are working on, they know what you are submitting, they know the results of your peer reviews. They control every part of the process and register every action you take."

Great work!

1/6 Super excited to share with you our work on Marchantia intra-specific diversity and pan-genomics, just out @naturegenet.bsky.social

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

Everything on the discoveries in the thread by @chloe-beaulieu.bsky.social

I want to emphasize 5 additional points:

Evolution of sexual systems and regressive evolution in Riccia The genus Riccia is the most speciose of the Marchantiopsida, the complex thalloid liverworts. In contrast to the predicted ancestral liverwort and the majority of extant liverworts that are dioicou...

Sex chromosime evolution in complex thalloid #liverworts from the perspective of #Riccia genomics. Both Riccia genomes were assembled using @nanoporetech.com Pore-C and native DNA sequencing:
nph.onlinelibrary.wiley.com/doi/full/10....

Seriously? 1M$ for Q20 short read machine?

Huge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀

Plus a whole bunch of updates for dorado polish and the odd misc bug fix.

github.com/nanoporetech...

We are pleased to share our work on the evolution of translation initiation now published in Nature Communications. Take a look at leaderless mRNAs and eS26 in the small ribosomal subunit of Saccharolobus solfataricus. rdcu.be/d5pgg

Mk1 family of @nanoporetech.com sequencers

That's true, but in vitro culture doesn't eliminate endophytes. There are some Riccia specific bacteria living in thallus.

Well, it's not that simple when working on bryophytes (collected in field) - in the best cases we got 60-65% of reads for nuclear genome, 3-7% of organellar genomes, 20-30% of contaminats (both endophytes and epiphytes).

New kid on the block 😎
Upgrade of our @nanoporetech.com mk1c

One cell is enough, the second one was for pore-C. When we resequenced another Riccia species, one minion fc provided only 15x coverage at single copy genes. But it was a field collected sample with alga and bacterial contaminants. Also these times we got only 12-16 Gbp from minion flow cells.

GitHub - tolkit/telomeric-identifier: Identify and find telomeres, or telomeric repeats in a genome. Identify and find telomeres, or telomeric repeats in a genome. - tolkit/telomeric-identifier

To identify the basic repeated telomeric unit, the telomeric-identifier v.0.2.41 (github.com/tolkit/telom...) was used with default parameters (1% of the length of the chromosome either side). 2031 AAAACT motifs were detected as telomeric repeat units.

Well, it's not gapless nor complete for sure, but the eight longest scaffolds correspond to Riccia fluitans genome. I started reassembly R. sorocarpa using Herro corrected reads and Verkko2 assembler/scaffolder.

Thanks David👍 We are working on comparison of all liverwort chromosome scale assemblies repeatomes, including our latest Apopellia 2.7 Gbp genome.

Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.) - Scientific Data Scientific Data - Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)

The first T2T assembly and annotation of #liverwort Riccia sorocarpa genome using only @nanoporetech.com technology. Done using 2 Promethion flow cells and one minion for cDNA sequencing. More to come soon...
www.nature.com/articles/s41...

Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains, carpathians) - Scientific Report... Scientific Reports - Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains,...

Some insight into biology and organellar genomics of rare #liverwort Arnellia fennica. Genomic data generates sorely using @nanoporetech.com technology:
www.nature.com/articles/s41...