Schneeberger Lab

1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!

Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...

Awesome new work from @labschneeberger.bsky.social (with a small contribution from the Weigel lab). Experimentally observed mutational patterns in centromeres underpin a model that recapitulates intra-specific centromere divergence!
www.biorxiv.org/content/10.1...

New preprint out from our lab, showing how mutations drive centromere evolution! 🧬
Check out this thread from Xiao Dong to learn more.

🍹In our new #PlantersPunch CEPLAS Postdoc Craig Dent from @labschneeberger.bsky.social @mpipz.bsky.social pz.bsky.social explains why the DNA of the European potato is at the same time diverse...and not diverse🤔! Very exciting story! One question remains: which one tastes best 🥔🍟😜?
➡️ bit.ly/42Mys6F

A Recipe for Complexity: Building the Potato Pan-Genome

Interested in hearing more about the story behind our latest paper?
Check out our blog post and the latest @naturepodcast.bsky.social episode!

📝 go.nature.com/3G73vT7

🎙️ www.nature.com/articles/d41...

🌱 This resource provides a foundation for genomics-assisted breeding in this challenging autotetraploid crop that feeds over a billion people globally, with particular utility for complex traits governed by multiple loci across different haplotypes!

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🍟 We demonstrate this by generating megabase-scale pseudo-genome assemblies for modern cultivars using only cost-effective short reads - including for 'Russet Burbank', THE famous French Fries potato!

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📊 Yet, our assemblies already cover ~85% of all European potato genetic diversity, indicating most haplotype diversity in Europe is already captured. To demonstrate practical utility, we converted the pan-genome into a haplotype-graph that enables megabase-scale phasing from short reads only!

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🌎 The explanation? While multiple bottlenecks during the potato’s journey from South America to Europe – and later the Irish Potato Famine – reduced haplotype diversity, the high sequence diversity likely stems from wild species introgressions during domestication.

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🧩 Paradoxically, despite the high sequence diversity, haplotype diversity was remarkably constrained. From 40 potential distinct haplotypes, we found an average of only 9 unique haplotypes per genomic region.

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🧬 We observed extreme sequence diversity between haplotypes of ~ 1 variant per 56 bp between haplotype pairs – the highest reported in any domesticated crop so far!

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The phased pan-genome of tetraploid European potato - Nature A haplotype-resolved pan-genome of autotetraploid European potato founder lines shows high nucleotide diversity at remarkably low haplotype diversity, which is probably the result of hybridization eve...

📢 Excited to share our work out now in @nature.com! 📢

We present the phased pan-genome of tetraploid European potato, based on 10 historical cultivars representing 85% of European potato diversity.

Learn more below!

🔗 www.nature.com/articles/s41...

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