Kuba Sawicki

Our latest paper, "Revisiting the Pellia sensu lato complex: an integrative review of taxonomic revision, phylogeny, and molecular biology," is now out in ASBP. It’s my final publication affiliated with the Dept. of Botany.
Check it out: www.journalssystem.com/asbp/Revisit...
#Bryology #Liverworts

I’ll try to figure something out next week.

It’s MGI T1+. PC workstation incoming soon.

Something new is coming to our lab 😎

Giant chromosomes of a tiny plant—the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta) AbstractBackground. The liverwort Apopellia endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability,

Tiny plant, giant genome! 🌱🧬

We’re excited to share the final version of our paper in @GigaScience: the first complete telomere-to-telomere (T2T) assembly of the liverwort Apopellia endiviifolia.
Thanks @ncn.gov.pl

Check out the full open-access study here: doi.org/10.1093/giga...

Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis | Microbiology Spectrum RNA modifications are increasingly recognized as critical regulators of host-virus interactions, yet their specific roles in human viral infections remain largely unexplored. Here, we provide the firs...

End of an era! 🧬 Our latest paper is out now in Microbiology Spectrum.
This marks our final study utilizing the @nanoporetech.com RNA002 chemistry before we transition to RNA004. It’s been a wild ride with those flow cells! 🧪📖
Read it here: journals.asm.org/doi/10.1128/...
#Nanopore #DRS #UWM

ok, email sent.

Are you still in Poland? PM me please, as I can't find your recent email address.

Are you interested in academic position (including teaching)?

The nap after lunch.
#wildlife #Butryny #Poland #Warmia

New genomic techniques: Council and Parliament strike deal to boost the competitiveness and sustainability of our food systems Council and Parliament reach provisional deal on a set of rules for new genomic techniques, aiming to improve the competitiveness of European agriculture and support the sustainability of our food sys...

www.consilium.europa.eu/en/press/pre...

Awesome

Nope, it's pure nanopore assembly (+Pore C). But the Swiss team used Hifi+Hi-C, the genomes are collinear, just more gapped than ONT assembly.

The @embo.org Workshop at the GMI and the @viennabiocenter.bsky.social has come to a close! From November 25th-27th, researchers attended inspiring talks and engaged in discussions on the topic of plant evolution. #EMBOplantEvo

Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta) AbstractBackground. The liverwort A. endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, genomic

Our paper “Giant chromosomes of a tiny plant” is out in @gigascience.bsky.social! We present a T2T genome assembly of the simple thalloid liverwort Apopellia endiviifolia with truly giant chromosomes. 🌱🧬 #plantgenomics #T2T #liverworts @nanoporetech.com
Thanks @ncn.gov.pl !

tinyurl.com/m8tkkxd3

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: