Groundbreaking Method for Affordable Construction of 1,000 Human Genomes Fuels Future of Medicine A new methodology for assembling over 1,000 human genomes significantly enhances our understanding of genetic diversity, promising advances in medicine.

Groundbreaking Method for Affordable Construction of 1,000 Human Genomes Fuels Future of Medicine #China #Hangzhou #Human_Genomes #Westlake_University #Pangenome

See how Novogene helped build a soybean pan-genome combining wild, landrace & cultivated accessions to uncover structural variation tied to yield, flowering & stress traits. A game-changer for crop genetics. #PlantGenomics #Breeding #PanGenome https://tinyurl.com/3fud3j9c

🌊🧬 #Freshwater #microbes in action! Scientists explored the pangenomes of Limnohabitans, Aquabacterium, and Novosphingobium to reveal their hidden hydrocarbon-degrading powers. #Microbiology #Pangenome #EnvironmentalScience
https://ow.ly/r3Uh50Yh1Nw

💡 #KnowledgeHighlight | Tutorial: #Pangenome Hackathon by @bioinfomics.bsky.social @inrae-france.bsky.social
pangenome-hackathon-genotoul-bioinfo-11d6d4f47ac33734abfa2a1377.pages-forge.inrae.fr/pages/tutori...

Explore more open-access training materials ➡️ knowledge.erga-biodiversity.eu

Validate User

Our paper "Panalyze: automated virus pangenome variation graph construction, analysis and annotation" is out in Bioinformatics Advances, link below

#pangenome #virus #pathogen #genomics

academic.oup.com/bioinformati...

A sorghum pangenome reference improves global crop trait discovery - Nature A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.

A #sorghum #pangenome reference improves global #crop trait discovery

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

#PlantScience @nature.com @lisa-sorghum.bsky.social @sorgguy.bsky.social @sorghumbase.bsky.social @pangenomics.bsky.social @nadiashakoor.bsky.social @sorghumandfennel.bsky.social @crop4clima.eu

#BPR
Pan-genome study of tea reveals JAZ stress genes vary widely across cultivars, with key members under positive selection.
Details: maxapress.com/article/doi/10.48130/bpr...
#Tea #PanGenome

It’s a colorful pangenome world - Nature Methods A pangenome can reveal the spectrum of genome variation within a species. The toolbox for working with pangenomes is filling up.

🧬 A #pangenome can reveal the spectrum of genome variation within a species. The toolbox for working with pangenomes is filling up, thanks to #BaskinEngineering researchers @khmiga.bsky.social, @benedictpaten.bsky.social, and @russcd.bsky.social.

Via @natmethods.nature.com: go.nature.com/4spcbHb

sqz - bioconda | Anaconda.org Install sqz with Anaconda.org. sqz is a tool for compressing and decompressing path annotations in GFA files.

sqz is now available in bioconda!

anaconda.org/channels/bio...

#pangenome #compression #bioinformatics

In the journal Horticulture Research, by assembling chromosome-level genomes of multiple representative cultivars and integrating them with existing references, the team generated graph-based and linear pangenome models.
#Papaya #Pangenome
Details: doi.org/10.1093/hr/u...

全面综述超级泛基因组在加速作物育种和改良方面的研究进展 🧬 🪴

🔗 mp.weixin.qq.com/s/joaeY9XAyE...

🔗 www.nature.com/articles/s44...

#Pangenome #super-pangenome #omics #genomics @natureportfolio.nature.com @abioticstress.bsky.social @sicb.bsky.social @planteditors.bsky.social @natrevbiodiv.nature.com @botanyone.bsky.social

Domestication gave us big fruits and higher yields - and quietly deleted genes for stress tolerance, adaptation, and who knows what else. Breeders can introgress traits from wild relatives, but now, super-pangenomes map where to look across entire genera. #pangenome

now out in Genomics, Proteomics & Bioinformatics

academic.oup.com/gpb/advance-...

doi: doi.org/10.1093/gpbj...

#pangenome #virus #evolution #mutation

Immune genes are “hard” because linear references can’t represent their diversity.

Graph-based references make those regions visible again.
That shift from linear to graph is foundational to everything we do at Benthic.

🔗benthic.bio/technology

#Genomics #HLA #Pangenome

See how Novogene helped build a soybean pan-genome combining wild, landrace & cultivated accessions to uncover structural variation tied to yield, flowering & stress traits. A game-changer for crop genetics. #PlantGenomics #Breeding #PanGenome https://bit.ly/49QL2Fe

Another beauty from our recent study!
𝐇𝐨𝐥𝐨𝐓𝐫𝐚𝐜𝐤𝐢𝐧𝐠 thousands of holocentromeres' synteny across 40 MY of evolution

Turns out holocentromeres can be stable in identity but wildly dynamic in structure. 🧬

If you want to read more about it, here: www.biorxiv.org/content/10.6...
#Centromeres #Pangenome

Haplotype comparison of the fully phased chromosome 9 uncovers a variety of evolutionary processes. Top: Explanation of the approach to assign haplotypes to accessory nodes of the pangenome and subsequent visualization: 1. create a pangenome graph and parse its variation; 2. the graph is transformed into a sequence alignment for visualization; 3. the core and unique nodes remain unchanged, while the accessory nodes are recursively assigned to different haplotypes. Middle: Pangenome graph of the phased chromosome 9 created with Minigraph-Cactus and visualized with Bandage. The nodes of the graph are coloured based on the haplotypes assigned in the bottom panel. Bottom: Alignment of haplotypes of chromosome 9 for all phased P. effusa isolates, derived from the pangenome graph in 4 kb windows, as described in the top panel.

#Plant pathogens secrete effectors to establish infections, but resistant crops select for resistance-breaking #pathogens. @mfseidl.bsky.social &co use #pangenome graph analyses of 19 resistance-breaking races of an #oomycete pathogen to identify several effectors @plosbiology.org 🧪 plos.io/4qA6nKC

Haplotype comparison of the fully phased chromosome 9 uncovers a variety of evolutionary processes. Top: Explanation of the approach to assign haplotypes to accessory nodes of the pangenome and subsequent visualization: 1. create a pangenome graph and parse its variation; 2. the graph is transformed into a sequence alignment for visualization; 3. the core and unique nodes remain unchanged, while the accessory nodes are recursively assigned to different haplotypes. Middle: Pangenome graph of the phased chromosome 9 created with Minigraph-Cactus and visualized with Bandage. The nodes of the graph are coloured based on the haplotypes assigned in the bottom panel. Bottom: Alignment of haplotypes of chromosome 9 for all phased P. effusa isolates, derived from the pangenome graph in 4 kb windows, as described in the top panel.

#Plant pathogens secrete effectors to establish infections, but resistant crops select for resistance-breaking #pathogens. @mfseidl.bsky.social &co use #pangenome graph analyses of 19 resistance-breaking races of an #oomycete pathogen to identify several effectors @plosbiology.org 🧪 plos.io/4qA6nKC

Haplotype comparison of the fully phased chromosome 9 uncovers a variety of evolutionary processes. Top: Explanation of the approach to assign haplotypes to accessory nodes of the pangenome and subsequent visualization: 1. create a pangenome graph and parse its variation; 2. the graph is transformed into a sequence alignment for visualization; 3. the core and unique nodes remain unchanged, while the accessory nodes are recursively assigned to different haplotypes. Middle: Pangenome graph of the phased chromosome 9 created with Minigraph-Cactus and visualized with Bandage. The nodes of the graph are coloured based on the haplotypes assigned in the bottom panel. Bottom: Alignment of haplotypes of chromosome 9 for all phased P. effusa isolates, derived from the pangenome graph in 4 kb windows, as described in the top panel.

#Plant pathogens secrete effectors to establish infections, but resistant crops select for resistance-breaking #pathogens. @mfseidl.bsky.social &co use #pangenome graph analyses of 19 resistance-breaking races of an #oomycete pathogen to identify several effectors @plosbiology.org 🧪 plos.io/4qA6nKC

Today and tomorrow at #PAG33 catch up with our scientists from the @ahalllab.bsky.social!

More details about their talks below 👇

#genomics #cropscience #pangenome

Primulina pan-genome reveals differential gene retention following whole-genome duplications and provides insights into edaphic specialization Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pa…

The Primulina #pangenome provides a resource for dissecting mechanisms underlying edaphic specialisation www.sciencedirect.com/science/arti... #biodiversity #genomics

Uncovering hidden phylo: and ecogenomic diversity of the widespread methanotrophic genus Methylobacter Abstract. The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater a

🚨 New paper out: Ecogenomics of Methylobacter 🦠

- three different MMOs to oxidize CH4 in single species
- machinery for nitrogen, sulfur, iron, and hydrogen metabolisms
- adaptations to low O2 conditions
...

led by @wutkowska.bsky.social

tinyurl.com/pmntwuk6
#MicrobeSky #pangenome

Comparative Genomics Reveals Multipartite Genomes Undergoing Loss in the Fungal Endosymbiotic Genus Mycetohabitans Abstract. Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they b

@bhuwanabbot.bsky.social @morgancarterphd.bsky.social @raw937.bsky.social @andrabuchan.bsky.social et al. present a pangenome analysis of the endofungal genus Mycetohabitans, showing bacteria-fungus coevolution.

🔗 doi.org/10.1093/gbe/evaf231

#genome #evolution #pangenome #MicrobeSky

Our PhD student Clémence Lauden is presenting her poster on Metapangenomic analysis within the Thermococcales at #Pangenome25 conference in Valencia🧬🌐

If you’re attending , don’t miss the chance to stop by, ask questions, and chat about the project.

See you there! 👋🎓
#pangenome #archaea

Home

We’re excited to announce the launch of the beta version of PanGBank website! 🧬🌐
pangbank.genoscope.cns.fr

PanGBank is a web-based platform for exploring, analyzing, and downloading pangenomes created with #PPanGGOLiN.

🔗 Dive in, test it out, and let us know what you think!

#pangenome

@genolabgem.bsky.social was there with @j-main-guy.bsky.social and @tlemane.bsky.social presenting the PanGBank database and new developments in metapangenomics #pangenome #PPanGGOLiN

Example of statistics obtained using the stats command on the NewRiceGraph MGC.gfa.gz graph: gratools stats -g NewRiceGraph MGC.gfa.gz A nice tabular format in rendered in the terminal, with path names, number of nodes, size, etc...

We are pleased to release today GraTools, an user firendly tools to manipulate the #pangenome variation #graph in GFA format.

@ird-fr.bsky.social @cirad.bsky.social @inrae-france.bsky.social

#Day3 of STOC Plant 2025 is kicking off with the second keynote by @ManuelSpannagl from @MU_CCFI_Biotech @MurdochUni 🇦🇺

Pan-Multi-Omics in Wheat: what can we learn? 🪴 🧬 🌾

#STOCPlant2025 #spatialomics #spatiotemporalOmics #omics #plantscience #PanOmics #Pangenome

Using pangenome variation graphs to improve mutation detection in a large DNA virus Accurately quantifying viral genetic diversity is essential for understanding pathogen evolution, transmission, and emergence. However, standard approaches that map sequencing reads to a single linear...

Our work on mapping read libraries to viral #pangenome variation graphs (PVGs) to reduce reference bias

Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example

"Using pangenome variation graphs to improve mutation detection in a large DNA virus"
www.biorxiv.org/content/10.1...
[1/7]

figure from the paper with a Venn diagram and a simple evolutionary tree

New #ISEPpapers! Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes www.cell.com/current-biol... #protists #algae #microbes #pangenome #genomics #evolution