RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments Abstract. Identifying recurrent changes in biological sequences is important to multiple aspects of biological research—from understanding the molecular ba

Robbins, Liu & Kelly present RECUR, a method for identifying recurrent amino acid substitutions from multiple sequence alignments that is fast, easy to use, and scalable to thousands of sequences.

🔗 doi.org/10.1093/molbev/msag036

#evobio #molbio #compbio

@thaisdalsasso.bsky.social is applying new tools to address the evolution and functional diversification of secreted proteins of fungal plant pathogen. Preprint here: www.biorxiv.org/content/10.6...

Evolutionary History and Diversification of M35 Metalloproteases in Dothideomycetes: A Phylogenomic Overview and Case Study in Corynespora cassiicola - Current Microbiology Deuterolysin metalloproteases (M35s), a family of zinc-dependent proteolytic enzymes, function as key virulence factors in bacteria and fungi. In plant-pathogenic fungi, these proteins induce host cel...

Happy to have contributed to this!
We investigated the #evolution of a virulence-associated gene family across Dothideomycetes, revealing duplication and loss events, including lineage-specific expansions in a crop pathogen. 🧬 #FungalGenomics

👉 DOI: doi.org/10.1007/s002...

Congrats @marco-guerreiro.bsky.social. @estukenbrock.bsky.social and colleagues on this exciting study linking codon optimization and adaptive translation to lifestyle transitions in a group of fungi.

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Wishing you all happy holidays. 🎄🎁
Greetings from the Environmental Genomics Group.
🇲🇽🇫🇷🇧🇷🇵🇹🇵🇪🇷🇸🇮🇷🇩🇰🇩🇪🤗

Personally, I’m very happy and proud to have contributed to this work during my postdoc at the University of São Paulo. Huge congratulations to Pedro Vilanova on his first first-author paper, and to our amazing PI Prof. Claudia Monteiro-Vitorello! 👏
#MPMI #FungalGenomics #Transcriptomics

🎉 Our new paper is out! We assembled a telomere-to-telomere genome 🧬 of Sporisorium scitamineum and showed how two smut strains with contrasting virulence deploy distinct early-infection programs on resistant and susceptible sugarcane genotypes. DOI: doi.org/10.1186/s128...

Had a great time organizing & teaching the MadFungi transcriptomics workshop. We spent three amazing days on RNA-seq for plant–microbe interactions and had great conversations with brilliant MSc/PhD students! 🌱🍄
#RNAseq #PlantMicrobeInteractions #Bioinformatics #PlantPathology

What Large Language Models Know About Plant Molecular Biology Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MoBiPlant, the first compreh...

Important read if you use LLMs for science knowledge discovery around plants "What Large Language Models Know About Plant Molecular Biology" www.biorxiv.org/content/10.1.... As per usual LLMs appear to propagate biases.

Molecular mimicry of plant cell-surface immune receptors by fungal secreted leucine-rich repeat proteins Leucine-rich repeat (LRR) receptor-like kinases (LRR-RLKs) are important plant immunity proteins. The wheat pathogen Zymoseptoria tritici produces many virulence effectors during infection; however, m...

Really happy this is out in preprint - Congratulations to @graemekettles.bsky.social @zymohaider.bsky.social, and everyone involved for their hard work completing this study! It examines a Z. tritici effector that is a molecular mimic of plant LRRs, and suppresses PTI www.biorxiv.org/content/10.1...

Genome-wide identification of conserved RNA structure in plastids The systematic discovery of functional RNA structure directly from sequence remains a central challenge in genomics. Plastid genomes, with their deep evolutionary history and extensive data availabili...

Dolly (@dollymehta.bsky.social‬) developed a pipeline to screen for conserved #RNA structures across genomes.
She then applied it ~14,000 #plastid genomes and identified nearly 60 conserved structures.

doi.org/10.1101/2025...

Great talk this afternoon by Joy Bergelson at #ESEB2025! 🌱 She showed how a small number of NLRs in Arabidopsis can recognize P. syringae, and how a protein interaction model can help explain ETI responses.

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

In #GENETICS, @3rdreviewer.bsky.social‬ and @smishra677.bsky.social‬ show it is possible to estimate recombination solely using the allele frequency spectrum and provide a genealogical interpretation of the results, showing how #MachineLearning can provide insights into biology.

buff.ly/emixz9W

mamp-ml: A deep learning approach to epitope immunogenicity in plants Eukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...

#2025ISMPMI 📣 In silico screening of PRR-epitope interactions is now possible!

Here, we developed mamp-ml to predict their immunogenic outcomes without structural context. Let's accelerate engineering plant receptors for robust resistance! 🚀🌱 Small 🧵

www.biorxiv.org/content/10.1...

A genomic perspective on fungal diversity and evolution Nature Reviews Microbiology, Published online: 30 June 2025; doi:10.1038/s41579-025-01195-6In this Review, Mondo and Grigoriev explore the central role of omics approaches to investigate the biology and evolution of fungi and understand phylogeny and how traits evolved over time within the fungal kingdom.

New online! A genomic perspective on fungal diversity and evolution

Admixture’s impact on Brazilian population evolution and health Brazil, the largest Latin American country, is underrepresented in genomic research despite boasting the world’s largest recently admixed population. In this study, we generated 2723 high-coverage who...

Admixture’s impact on Brazilian population evolution and health | Science www.science.org/doi/10.1126/...

Transcriptomics in the era of long-read sequencing Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00828-zAdvances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including experimental and computational tools, current applications, challenges and opportunities.

FYI: New online! Transcriptomics in the era of long-read sequencing

Genomic and genetic insights into Mendel’s pea genes - Nature Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...

The rest of Mendel's alleles characterized! So, out of 7 traits, 3 caused by TE insertions!!! (though apparently there are two different green alleles, one cause by a TE insertion, but another a promoter deletion allele)

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

A phylogenetic approach to comparative genomics - Nature Reviews Genetics Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The authors review the application ...

Comparative genomics needs to use phylogenetic methods: why, how and common questions www.nature.com/articles/s41... @annadewar.bsky.social @lauriebelch.bsky.social