Latest posts tagged with #PanGenome on Bluesky
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
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
🧬 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 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
The Primulina #pangenome provides a resource for dissecting mechanisms underlying edaphic specialisation www.sciencedirect.com/science/arti... #biodiversity #genomics
🚨 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
@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
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
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...
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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
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
To obtain a clear, non-biased view of #biodiversity, a #pangenome approach is mandatory...
🌐 New PCI Genomics recommendation: GrAnnoT enhances annotation transfer via pangenome graphs, connecting linear and graph-based genomes. 🔬 “a valuable pangenome toolkit addition — fast, conservative, reproducible.” ➡️ genomics.peercommunityin.org/articles/rec... #Pangenome #OpenScience
Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence. #MycobacteriumTuberculosis #Pangenome #ReferenceSequence @biorxivpreprint.bsky.social 🧪
www.biorxiv.org/content/10.1...
