Osiel Gonçalves 💻🧬🧪🌱🍄

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data - Nature Communications High-throughput sequencing retrieves viral sequences from diverse environments, but these sequences can be difficult to classify. The here developed VITAP is a taxonomic assignment pipeline for DNA an...

VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data www.nature.com/articles/s41... #jcampubs

Expanding the human gut microbiome atlas of Africa - Nature A cross-sectional study from four African countries shows the importance of investigating the gut microbiome in previously under-represented populations and provides a framework for equitable microbio...

Out now in @nature.com: Gut microbiome diversity across African populations - a valuable resource for further research and foundational for global health equity. 🧪

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

DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes - BMC Bioinformatics Background Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to...

DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes bmcbioinformatics.biomedcentral.com/articles/10.... #jcampubs

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...

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome - Nature Microbiology Thousands of metagenome-assembled genomes from the Vanishing Glaciers project showcase the interactions between prokaryotes, algae, fungi and viruses in glacier-fed stream environments.

OUT NOW: Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

by Gregoire Michoud, Tom Battin & co

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

Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons - Nature Microbiology Structural and phylogenetic analyses show that programmable RNA modifications ubiquitous in archaea and eukarya arose from bacterial transposons.

OUT NOW: Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons

by Samuel Sternberg, @audeber.bsky.social & co

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

A timeline titled "The Golden Age of Antibiotics" shows when each antibiotic drug class was first available for medical use, with example antibiotics labeled. Classes are color-coded by their source: actinomycetes, other bacteria, fungi, or synthetic. Milestones include the first antibiotics (arsphenamines in 1910), as well as the discovery of many actinomycetes-derived antibiotics, such as streptomycin, and sulfonamides, penicillins, and tetracyclines. Data: Hutchings, Truman, Wilkinson (2019). Created by Saloni Dattani for Our World in Data.

Many people talk about the "Golden Age of Antibiotics", but I hadn't seen it visualized properly.

Just how many types of antibiotics were discovered during that time?

So, I visualized it myself!

Osiel Silva Gonçalves | Achievement See this researcher's achievement on ResearchGate.

www.researchgate.net/profile/Osie... via @researchgate

SCARAP: scalable cross-species comparative genomics of prokaryotes AbstractMotivation. Much of prokaryotic comparative genomics currently relies on two critical computational tasks: pangenome inference and core genome infe

SCARAP: scalable cross-species comparative genomics of prokaryotes. #ComparativeGenomics #Genomics #ProkaryoteGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Functional and evolutionary significance of unknown genes from uncultivated taxa Nature - We analysed 149,842 environmental genomes from multiple habitats and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel gene families exclusive to...

"Functional and evolutionary significance of unknown genes from uncultivated taxa", a publication from the lab of @jhcepas.bsky.social (2023), highlights what can be achieved by integrating GMGC and other gene catalogs to hunt for novel gene families in 150k genomes

www.nature.com/artic...

Logo of OrthoHMM, a novel software for HMM-based inference of orthologous groups of genes

Benchmarking analysis of OrthoHMM and previously published algorithms. OrthoHMM has better precision, recall, and FMI scores. Benchmarking was conducted against the Orthobench dataset of expertly curated orthogroups

NEW preprint!🥳

Orthogroups are a prerequisite for comparative genomics and Tree of Life inquiries

Introducing #OrthoHMM, software that improves the inference of orthogroups (blue in fig)

OrthoHMM may refine our understanding of genome evolution and the Tree of Life

🔗 tinyurl.com/4s9mwxz6

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Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer Giant transposons called “Starships” mediate horizontal gene transfer in fungi to drive repeated evolution and rapid adaptation.

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer
Science Advances
www.science.org/doi/10.1126/...

Cell envelope diversity and evolution across the bacterial tree of life - Nature Microbiology This Review discusses the diversity of cell envelope architectures across major bacterial phyla and highlights conserved features found in diderm lineages.

Nice Review Article published this year in Nature Microbiology:

Cell envelope diversity and evolution across the bacterial tree of life

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

www.researchgate.net/profile/Osie... via @researchgate