🚨 Last seats alert!

Join our Computational #Pangenomics online course with @andreaguarracino.bsky.social, 13–16 April, to learn how to build & analyse pangenome graphs from whole genome assemblies.

www.physalia-courses.org/courses-work...

#Bioinformatics #Genomics #DataScience #RStats

The 2nd edition of the Computational #Pangenomics course with @andreaguarracino.bsky.social is almost full.

If interested, check it out: www.physalia-courses.org/courses-work...

#Pangenomics #Bioinformatics

Trippy Memphis bridge https://pangenome.github.io/MemPanG26/

Level up your #pangenomics game! Workshop, conference & biohackathon in #Memphis, May 11-15, 2026. Join us and get your hands dirty with sequence alignment, explicit and implicit graphs, cutting-edge methods, and AI. Register now! pangenome.github.io/MemPanG26/ #Bioinformatics #MemPanG26

Release Updated algorithm · codialab/sqz What's changed Rewrite of the main algorithm, this version should be both faster and fixes a couple of issues were the old version ran into problems with certain graphs. Additionally, it adds funct...

🚀 SQZ v0.2.0 released!

🔄 Rewritten core algorithm → faster + more robust (fixes graph edge cases)
✨ New commands:
• compress-partial
• compress-additional
• compress-full (now works on compressed graphs)
• check-compressibility
• test

🔗 github.com/codialab/sqz...

#pangenomics #compression

Deadline tomorrow! Explore how advances in the field of #pangenomics are transforming genome #evolution, population #genetics and more in the EMBO Practical Course "Pangenomics" in Campania region, IT, 7–13 June 2026.

https://meetings.embo.org/event/26-pangenomics
#EMBOPangenomics #EMBOevents 🧪

This figure displays the systematic development of the super-pangenomes, which is based on widely used methods and integrates raw genomic data, biological insights, and advanced breeding applications to increase crop tolerance and productivity. The process includes six key steps: (1) initial data acquisition involves various high-throughput sequencing methods to capture genomic complexity and structural variations (SVs); (2) the information identified in the next step serves as the foundation for understanding genetic diversity and evolutionary adaptations across species; and (3) the extracted genomic features are integrated into variation networks, regulatory elements affecting gene expression, epistatic interactions, trait-associated variant catalogs, functional gene annotations, and panomics to harness genotype-phenotype relationships. This stage enhances the discovery of key functional genes linked to agronomic traits, stress tolerance, and breeding targets. (4) In the next step, the integration of panomics datasets leads to super-pangenomics (a surprise package), which provides new insights into hidden genetic diversity across multiple species. This comprehensive analysis serves as a genetic toolbox for fast-forward breeding strategies: (5) the super-pangenomes facilitates diverse GAB methods that can accelerate crop domestication and improvement; and (6) in the final stage, by leveraging these comprehensive resources, we can achieve the final goal of climate-smart, high-yielding crops with enhanced abiotic stress tolerance, biotic stress resistance, and agronomic trait improvements. Created with BioRender.com.

A multistep process for super #pangenomics to deliver improved #crop cultivars

🔗 www.nature.com/articles/s44...

#Genomics @tpg-sssa.bsky.social @innovativegenomics.bsky.social @planteditors.bsky.social @scinews.bsky.social @scinews.bsky.social @botsocamerica.bsky.social @plantevolution.bsky.social

📣 Registration is now open for the International Genome Graph Symposium (IGGSy) 2026 in Ascona, Switzerland; July 5-9, 2026

🗓️ Register by Feb 16

🤝 Cutting-edge genome graph science & lively discussions

🔗 Website: iggsy.org

#IGGSy26 #GenomeGraphs #Pangenomics

Sex without crossovers mimics clonal reproduction in the holocentric plant Rhynchospora tenuis Meiotic recombination ensures accurate chromosome segregation and promotes genetic diversity by generating crossovers between homologous chromosomes. While essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy. However, obligate achiasmy in both sexes of a sexual species has not been previously documented. Here, we investigate the beak-sedge Rhynchospora tenuis, a holocentric plant with the lowest known chromosome number among flowering plants (n = 2) and inverted meiosis. Using chromosome-scale genome assemblies from nine accessions, molecular cytogenetics, immunocytochemistry, high-throughput single-gamete sequencing and whole-genome sequencing of controlled crosses, we show that R. tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis. Despite normal early meiotic axis formation, synapsis fails, crossovers are not detected cytologically or genetically, and univalents persist at metaphase I. Extensive haplotype-specific accumulation of transposable elements (TEs) generates segregation distortion (e.g. meiotic drive), favouring the transmission of larger, TE-rich chromosomes. Remarkably, sexual reproduction is retained with fertilisation producing viable seeds only when translocation-compatible gametes meet, indicating strong post-meiotic selection that eliminates incompatible homozygous combinations. As a result, all surviving offspring are genetically identical to the maternal genotype, effectively restoring heterozygosity each generation and mimicking clonal reproduction. We propose that the combined effects of recombination loss, low chromosome number, holocentricity, inverted meiosis, and selective transmission of longer chromosomes enable faithful segregation and clonal-like inheritance despite sexual reproduction. These findings challenge the boundary between sex and clonality, revealing a unique evolutionary strategy linking genome architecture, recombination loss, and transmission bias. ### Competing Interest Statement The authors have declared no competing interest.

3️⃣ Sex without crossovers mimics clonal reproduction in Rhynchospora tenuis

🌱 An extreme meiotic outcome: faithful segregation without crossovers in a holocentric plant.
🔗 doi.org/10.64898/202...

#Preprint #GenomeEvolution #Meiosis4eva #centromere #Pangenomics

Want to learn about #Pangenomics?

Join us in April for the 2nd edition of the #ComputationalGenomics course with @andreaguarracino.bsky.social

Check it out: www.physalia-courses.org/courses-work...

Engineer for the development of new methods in pangenomics - LABGeM Prokaryotes —bacteria and archaea— are diverse, ubiquitous organisms with vast impacts on health, soil, and ocean ecosystems. Large-scale genome sequencing and pangenomics have revealed their molecula...

📢 Hiring: Bioinformatics Engineer position funded by the ANR PanGAIMiX, for the development of new methods in the PPanGGOLiN software suite.

💻 Build cool tools for #pangenomics
🔬 computer science × biology

📍 Evry, France | ⏳ Fixed-term contract
👉 Interested? Contact us
🔗 bit.ly/3NfSP8o

Pangenomics in the Mimulus guttatus Species Complex Click on the article title to read more.

📢 New publication ' #Pangenomics in the Mimulus guttatus Species Complex' by Maddie James in Molecular Ecology Resources 🧬🧪

doi.org/10.1111/1755...

Panorama: a robust pangenome-based method for predicting and comparing biological systems across species Over the last decade, the expansion in the number of available genomes has profoundly transformed the study of genetic diversity, evolution, and ecological adaptation in prokaryotes. However, traditio...

🔍 Want to dive deeper?
Read the preprint and try the tool:
📄 doi.org/10.64898/202...
💻 github.com/labgem/PANOR...

@ifb-elixir-fr.bsky.social @genoscopeumr.bsky.social @genopole.bsky.social
#Bioinformatics #Pangenomics #Genomics

Poster advertising “Earlham Institute at PAG33,” 9–14 January 2026, over a background image of green wheat. It lists four talks with speaker photos: Rachel Rusholme-Pilcher (Senior Postdoctoral Researcher) on pangenome graph-building tools for hexaploid wheat, 9 Jan, Wheat Genomics to Breeding session; Connor Reynolds (PhD Researcher) on ensemble models for analysing plant circadian time in bulk and single-cell RNA-seq data, 9 Jan, Systems Biology and ML session; Anthony Hall (Head of Plant Genomics) on de novo annotation revealing transcriptomic complexity across the Wheat 10+ Genomes, 10 Jan, International Wheat Genome Sequencing Consortium session; and Charles Dickinson (PhD Researcher) on population-scale genomics for coriander breeding, 10 Jan, Apiaceae session.

🌏 Heading to #PAG33 in January? Hear from the Anthony Hall Group who will be sharing their recent work generating the first wheat pan-transcriptome, developing new tools for #pangenomics, and using #machinelearning models in the study of the plant #circadianclock.

Explore how advances in the field of #pangenomics are transforming genome #evolution, population #genetics and more in the EMBO Practical Course "Pangenomics" in Campania region, IT, 7–13 June 2026.

Deadline: 3 February

https://meetings.embo.org/event/26-pangenomics
#EMBOPangenomics #EMBOevents 🧪

@tlemane.bsky.social presented PanGBank at #Pangenome25 conference in Valencia 🧬🌐

We’re thrilled to share this resource with the community and to see the growing interest in #pangenomics

We’ve just released a set of Google Colab tutorials to help you get started with PanGBank. 🧬💻
github.com/labgem/PanGB...

Whether you're new to the resource or looking to dig deeper, these step-by-step notebooks make it easy to jump in.

🔗 Try them out and tell us what you think!
#pangenomics

A possible pipeline for the uses of a pangenome graph. This pipeline can be roughly divided into three main sections (on the right): build a graph, using it, and adding reads. A first pangenome graph is created, usually with almost complete haplotype as- semblies. Since graph creating methods vary, and may be fraught with errors (unaligned regions, broken paths), assessing the quality of a graph is useful (this can be applied after each subsequent step). Similarly, it is also crucial to be able to visualize the graph, espe- cially on particular loci of interest (can also be done throughout the pipe-line). The graph can be augmented with additional data increasing allele counts, including known con- tig alignment or read mapping. Several augmentation iterations, with different types of data, can be considered. Since most analyses focus on genes and transposable elements, it is usually useful to add an annotation (available on one or several reference genomes), which projected to the graph. This graph, possibly extended with new variants and an- notation, should be then shared with the community, following FAIR practices. Most analyses then focus on graphs with only one species, and the graph can be analyzed in order to find regions of interest. However, dual pangenomics, which studies the joint diversities of two species, can be envisioned. More generally, many species can also be modeled, for instance in the case of meta-genomics. Low coverage sequencing data of individuals can be compared or aligned to the graph in order to produce large genotyp- ing sets enabling population genetics studies (i.e. coalescence, association). Other omics (e.g. RNA-Seq, ChIP-Seq, Hi-C, LC-MS, BS-Seq etc.) data can be added to the graph, and potentially aggregated to multi-omic layers.

With many colleagues, we tried to gather the future prospects and challenges for #Pangenomics and #Pangenome research in agronomy, that can however be adopted more largely

hal.science/hal-05357866/

@ird-fr.bsky.social @inrae-france.bsky.social #FAIR #OpenScience #vizu

Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs A key application of pangenome graphs is the characterization of small and large genomic variants represented as bubbles within the graph. Although bubbles have been extensively studied in directed gr...

Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs
doi.org/10.1101/2025...

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...

#Genomics #Bioinformatics #Pangenomics

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic inf...

Yesterday, Nina Marthe, our wonderful PhD student with Matthias Zytnicky, resubmit our tool GrAnnoT, for pangenome variation graph annotation!

@ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻

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

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic inf...

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
doi.org/10.1101/2025...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...

#FunctionalGenomics #PlantSci #Pangenomics

School of Biological Sciences, University of Edinburgh. Pic by Katja Noskova

A dream came true as I started recently a postdoc in Edinburgh, @ simonmartinlab.org! I study the role of #chromosomal #inversions in #adaptation - especially in changing environments; involving #popgen, African monarch #butterfly #pangenomics & #SLiM. Big thank you #skr for making this possible.

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures. #SomaticVariantDetection #VariantCalling #Pangenomics #Genomics #Bioinformatics @biorxiv-genomic.bsky.social
www.biorxiv.org/content/10.1...

Join us for the 2nd edition of the Computational #Pangenomics online course, 13–16 April with @andreaguarracino.bsky.social.
You can learn how to build and analyse pangenome graphs from whole genome assemblies.

www.physalia-courses.org/courses-work...

#Pangenomics #Bioinformatics

Thanks to everyone who joined the #HackPR25 biohackathon following the @humanpangenome.bsky.social annual meeting in #Memphis. We hacked on #pangenome representation and interrogation for "laptopable" pangenome-scale analyses. Accessible #pangenomics is coming!

Graphics image showing webinar at EMBL-EBI about Inferring bacterial pangenomes with gene-based approaches. The webinar will run on 15 October 2025 at 14:30 BST. The speaker is Neil MacAlasdair. Image credit: Karen Arnott and Rebecca Nicholl, EMBL-EBI

Join us next week to discover how gene-based methods unlock the bigger picture of bacterial pangenomes.
Registration is free but essential:
www.ebi.ac.uk/training/eve... #pangenomics #bioinformatics #Genomics #BacterialResearch @embl.org @ebi.embl.org #webinar

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures.#SomaticVariantDetection #HapMap #Pangenomics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

Pangenomics and single-cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine. #Pangenomics #GrapevineGenome #ContinuousBearing @horticulturer.bsky.social
academic.oup.com/hr/advance-a...

Pangenome-guided sequence assembly via binary optimisation De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which c...

Pangenome-guided sequence assembly via binary optimisation
doi.org/10.1101/2025...

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...

#Pangenomics #DataScience #Bioinformatics #PlantSci

A pleasure and privilege to teach at the International #Bioinformatics Workshops #TIB2025 on #Pangenomics and #Phylogenomics at @ccg_unam with these motivated and talented participants from 🇵🇪, 🇨🇷, and 12 Mexican 🇲🇽 States. Find the course's contents available on #GitHub 👉 tinyurl.com/4um82sbn #UNAM👏👏👏

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet Most crop plants, including sugar beet ( Beta vulgaris subsp. vulgaris ), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wi...

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...

#Genomics #Bioinformatics #BigData #DataScience #Evolution #Phylogenomics #Pangenomics #LongReadSequencing