For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]

A flowering plant has been confirmed as a new carnivorous lineage, says research in Nature Communications. Findings show Saxifraga candelabrum can attract, trap, & digest insects, and absorb nitrogen from them, supporting prediction made by Charles Darwin: spklr.io/63323EuqgT #Biology 🌾 🧪

Identification of carnivory in the flowering plant Saxifraga via multidisciplinary evidence - Nature Communications

Carnivorous plants capture and digest insects for nutrients, an adaptive strategy typically found in wetlands. This study identifies carnivory in the alpine Saxifraga plant lineage, supporting Darwin's hypothesis of carnivory in this genus.

spklr.io

Absolute tour de force led by @ymalovichko.bsky.social, with contributions from many in the lab @leonhilgers.bsky.social @xuelingyi.bsky.social @mich-albertini.bsky.social Alejandro Gonzales-Irribarren, Evgeny Leushkin and many others Check #TOGA2 out: github.com/hillerlab/TO...

GitHub - hillerlab/TOGA2: TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments

TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments - hillerlab/TOGA2

github.com

Michael Hiller@hillermich.bsky.social · 2mo ago

The #TOGA2 preprint is now at www.biorxiv.org/content/10.6.... Describes the new method and the comparative genomics resource (annotations, orthologs, gene losses/dups, retrogenes and more) generated using a total of 9420 TOGA2 runs for 2173 vertebrate genome assemblies.

Had such a good time at @official-smbe.bsky.social talking about museum samples and comparative genomics. Many thanks to everyone who reached out to me and my supervisor for all her support @astridboehne.bsky.social. Special thanks to the Alexander-Koenig-Gesellschaft for funding my trip. #SMBE2026

For those interested in PacBio's SPRQ-Nx chemistry and reusable SMRT Cells: in the Genome of Sweden project, we moved from 2 to 3 acquisitions per SMRT Cell in June. The results are impressive—we’re now approaching 400 Gb HiFi yield from a single SMRT Cell!

Excellent dive into the bizarre world of turtles and how they completely reworked their bodyplan through gene loss by @leonhilgers.bsky.social #SMBE2026 Especially great detective work on the genes of interest!

If you are interested in #PacBio #HiFi sequencing of challenging specimens through long range #PCR amplification, check out my poster (Board 038, Blomster Salen) this evening between 6-8pm! #SMBE2026

Happy to announce the release of TOGA2 data for 68 turtle genomes, generated with a cryptodiran and a pleurodiran turtle reference. The combined TOGA2 annotation consistently improves annotation completeness compared with RefSeq. All data at genome.senckenberg.de/download/TOGA2. Genome browsers ...

Drivers of cold adaptation and genome evolution in Antarctic fish, and a haplotype resolved assembly for an important model notothenioid species 🐟 🧬 Our new paper available on BioRxiv #BiodiversityGenomics #ColdAdaptation www.biorxiv.org/content/10.6...

And the winner is… Your 2026 International Mollusc of the Year is 𝘾𝙪𝙢𝙞𝙖 𝙞𝙣𝙩𝙚𝙧𝙩𝙚𝙭𝙩𝙖, the Vampire Snail! It will be the first blood-feeding mollusc to ever have its genome sequenced. Huge thanks to the nominators & @sgn.one for unlocking its DNA secrets! 🧬🩸 #IMOY26

We now have genome browsers on our UCSC mirror at genome.senckenberg.de for the 1033 mammal and 866 bird assemblies, showing spliceAi, reference-based and ref-integrated TOGA2 tracks. Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html

Here's a genome from the Vertebrate Genomes Project (vertebrategenomespro...): a chromosome-level assembly for the false killer whale (Pseudorca crassidens)! 🐋 This resource advances cetacean research and conservation. Photo: Stefan Thiesen Buntrabe 1/2

New preprint out!!📜 We show that decades-old FFPE brain tissue archived in the unique Danish Brain Collection (up to 73 years old) can yield biologically informative genomes and transcriptomes. Read the full manuscript at: www.biorxiv.org/content/10.6... #RNA #DNA #FFPE #Brain

Lernt den Spitzenprädator Triplofusus giganteus kennen! 👹 Die Florida-Pferdemuschel ist mit einer Länge von bis zu 60 cm eine der größten fleischfressenden Schnecken der Welt. Sie nutzt ihren massiven Fuß, um ihre Beute zu „ersticken“. 🌊 Stimmt für den Atlantikriesen 👉 https://sgn.one/moty2026 🐚

I've always been fascinated with biodiversity, dreaming of discovering new species. That dream has finally come true: We found two new crab species tugged away in small streamlets in Guangdong! This journey started 7 years ago, huge thanks to Chao for taking me along! 🦀 🦀 🦀 doi.org/10.6620/ZS.2...

I wrote a short Nature Methods News & Views piece on deep learning based gene finders such as ANNEVO. www.nature.com/articles/s41...

Learning genes deeply - Nature Methods

Annevo uses deep learning to achieve unprecedented accuracy in eukaryotic gene annotation, approaching the performance of evidence-based methods.

nature.com

I hear you want novelty🦎->🐢, chromosome evolution 🧬, sex determination🩷, link population history📈 & climate🌏🌡️? Or you share my love for wonderfully weird animals? Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance www.biorxiv.org/content/10.6... A 🧵

Truly breathtaking work here, building on the concept of targeted sequencing and turning it dynamic. Remains to be seen how QV will scale beyond human/mammalian data, but the future of routine T2T assemblies might be around the corner: www.nature.com/articles/s41...

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications

Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

nature.com

Happy to share that our work with Ekaterina Osipova, @maggiemcko.bsky.social, Tim Sackton, Maude Baldwin & fantastic collaborators on convergent and lineage-specific genomic adaptations in sugar-feeding birds is published in Science www.science.org/doi/10.1126/.... While high sugar intake ...

Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds

High-sugar diets cause human metabolic diseases, yet several bird lineages convergently adapted to feeding on sugar-rich nectar or fruits. We investigated the underlying molecular mechanisms in hummin...

science.org

Our paper on foldback artifacts in long-read sequencing is now published in BMC Genomics! We introduce Breakinator to flag foldback and chimeric artifacts across library types, sequencers, and chemistries. Paper: link.springer.com/article/10.1... With Matthew Meyerson and @lh3lh3.bsky.social

Detecting foldback artifacts in long-reads - BMC Genomics

Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

link.springer.com

Say hello to Nallo - our Nextflow pipeline for long-read WGS analysis!👋 It handles both ONT and PacBio data and we’re using this for rare disease and population projects in Sweden. A big team effort by Felix Lenner, Anders Jemt et al.🧬💻 academic.oup.com/bioinformati...

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis

AbstractMotivation. Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics, due to its capacity to generate co

academic.oup.com

The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action: Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio

Aguilar-Gómez et al. use exome sequencing of 347 strawberry poison frogs to uncover the genetic basis of color variation. They identify that kit, ttc39b, and bco1 underlie blue-red, yellow-red, and gr...

cell.com

Amazing to see read N50 in the 100s of kb: www.sciencedirect.com/science/arti... Also, optimizing the protocol for long-fragment DNA extraction must have been a mighty effort!

Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly

The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore T…

sciencedirect.com

Just in time for Karneval, we present coelsch ! 🎭🥳 A platform-agnostic framework for single-cell recombination analysis. We study crossover variation in mutants & natural lines, identifying the largest natural inversion in A. thaliana to date! 📄 doi.org/10.64898/202... 🐱 github.com/schneeberger...

That looks great! To avoid errors due to starting with spotty gene annotations (gene loss vs. not annotated), I would suggest re-annotating every genome used with TOGA2 from the Hiller lab: github.com/hillerlab/TO... Many annotations out there are not optimal and TOGA2 has great power and accuracy.

GitHub - hillerlab/TOGA2: TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments

TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments - hillerlab/TOGA2

github.com

Laurie Belcher@lauriebelch.bsky.social · 7mo ago

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

📣 #Forschungsnews: Feine Unterschiede – 5 neue Krebsarten in der Nordsee entdeckt 🌊🦐 In der Deutschen Bucht, einem der weltweit bestuntersuchten Meeresgebiete, hat ein Senckenberg-Forschungsteam 5 neue Arten winziger Krebstiere nachgewiesen. Unbekannte Vielfalt vor der Haustür! 👉 https://sgn.one/1df

Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...

Megan Dennis@mydennis.bsky.social · 2y ago

Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).

Day 2: bringing the consortium researchers & experts together is on the theme of Functional & comparative genomics Keynote #StefanMundlos: Functional Genomics of Bat Limb Development With Genome Chalk team talks #LucasCanesin, #YuryMalovichko, #AlejandroGonzales, #BernhardBein & #MicheleAlbertini

⚡ We've released a new version of rdeval! v0.0.8 includes full support for @pacbio.bsky.social CiFi read preprocessing, visualization report improvements, and upgrades to performance and parallelization! 🔗 Release notes and source code: github.com/vgl-hub/rdev...

Release rdeval v0.0.8 · vgl-hub/rdeval

Changes in this Release New Features Added full support for PacBio CiFi read preprocessing, including CiFi-specific metrics, biologically precise cut-site handling, examples, and test datasets. Re...

github.com

Earth BioGenome Project 🌍@ebpgenome.bsky.social · 10mo ago

🌍✨ As sequencing ramps up, how will EBP-affiliates keep quality high? By building smarter, scalable tools and infrastructure to manage a global flood of genomic data. 💻🧬 📖👉Evaluation of sequencing reads at scale using rdeval: academic.oup.com/bioinformati... @vertebrategenomes.bsky.social

Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...