Noe Cochetel
@ncochetel.bsky.social
📤 202
📥 745
📝 2
Staff Research Associate @ UC Davis 🌱🍇🧪🧬🖥️
#PlantScience
#Genomics
Grape (pan)genomics
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Noe Cochetel
Molecular Biology and Evolution
9 days ago
@ncochetel.bsky.social
&
@cantulab.bsky.social
publish a new MBE Review on plant pangenomes, outlining major paradigms and showing how graph-based frameworks enable analyses that are difficult with single linear references. 🔗
doi.org/10.1093/molbev/msag087
#evobio
#molbio
#pangenome
#PlantSky
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Noe Cochetel
Brady Lab
over 1 year ago
Does anyone have experience with low-input high-throughput (96 well plate) RNAseq library preparation from plants (bonus points if it is with plant roots...)
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Noe Cochetel
PlantEvolution 🌱🌾
over 1 year ago
New preprint: Chloroplast and mitochondrial
#pangenome
of
#Arabidopsis
thaliana! Work led by
wenfeixian.bsky.social
#plantscience
www.biorxiv.org/content/10.1...
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Noe Cochetel
Jeffrey Ross-Ibarra
over 1 year ago
Postdoc jobs in the Gaut lab! Brandon isn't on here, so I can be frank: he is fantastic. I did my postdoc with him and he is not only an amazing scientist but one of my favorite humans. I would have happily stayed in his lab forever if that was feasible.
recruit.ap.uci.edu/JPF08999
#plantscijobs
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Noe Cochetel
UCDavisPlants
over 1 year ago
🍇 Dario Cantu, Mélanie Massonnet and Noé Cochetel collaborated on ways wild grape
#genomics
unlocks climate resilience for viticulture. Advances in pangenomics & haplotype analysis reveal traits for disease resistance, adaptability, & sustainability. ▶️
www.cell.com/trends/genet...
#ClimateAdaptation
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The wild side of grape genomics
With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture’s climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species’ adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.
https://www.cell.com/trends/genetics/fulltext/S0168-9525(24)00101-X
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Abstract finally out: "Phased Epigenomics and Methylation Inheritance in the Diploid Genomes of Vitis Vinifera". Learn more during the Grape Genome Initiative session at
#PAG32
in January 2025!
plan.core-apps.com/pag32/abstra...
over 1 year ago
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Noe Cochetel
GrapeGenomics
over 1 year ago
Grapegenomics is now live on BlueSky, all the news related to
grapegenomics.com
will be posted here. Follow to stay up to date on new grape, pathogen, and pest data!
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grapegenomics.com
https://grapegenomics.com
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Noe Cochetel
Dario Cantù
over 1 year ago
New preprint from the lab
biorxiv.org/content/10.1...
describing the conservation of the grape sex determining region (SDR) across angiosperm genomes and detailed history within Vitaceae leading to dioecy in Vitis and Muscadinia. Collaboration with
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Evolutionary history of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae
Dioecy, defined by the presence of either female or male flowers on separate individual plants, is rare in angiosperms. However, it has independently evolved multiple times from hermaphroditic ancesto...
https://biorxiv.org/content/10.1101/2024.11.10.622717v1
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Noe Cochetel
Phil Ewels
over 1 year ago
Feels like momentum is building over here recently 🦋 I set up
@nextflow.io
,
@multiqc.info
,
@openscience.software
and
@seqera.io
today - can't promise how active they'll be, but at least there are accounts to follow 😊 And of course,
@nf-co.re
has been here for a while already 🍏
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Noe Cochetel
Jo Wolfe, PhD
about 2 years ago
Wow! The complex genomic and epigenetic variation that builds the tasty diversity of Brassica oleracea (the single species that forms broccoli, cauliflower, kale, cabbage, Brussels sprouts) 🧪🥦🥬
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Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea - Nature Genetics
De novo genome assemblies of 22 Brassica oleracea accessions and pan-genome analyses highlight the effects of structural variations on gene expression and their contributions to morphotype diversifica...
https://www.nature.com/articles/s41588-024-01655-4
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#starterpacks
was a great resource for me to find researchers and feeds relevant to my area of research. You can browse them here:
blueskydirectory.com/starter-pack...
I hope to see
#GrapeGenomics
folks translocating here too 🍇🧬🖥️ !
over 1 year ago
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Noe Cochetel
Marc Somssich
over 1 year ago
Hello new Plant Scientists, 2 Things: 👉 To connect to 150 Plant Science Accounts and 3 relevent feeds, here's a
#StarterPack
for you:
go.bsky.app/8Zfmwf7
👉 To get your
#PlantScience
posts into the Plant Science Research Feed (here:
bsky.app/profile/did:...
), always use the Hashtag
#PlantScience
add a skeleton here at some point
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Stephen Turner
over 1 year ago
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you!
go.bsky.app/B5YYBfq
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Genomics+Bioinformatics Starter Pack 🧬🖥️
Join the conversation
https://go.bsky.app/B5YYBfq
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Noe Cochetel
Jeremy Allen
over 1 year ago
Wow. It has been just 3 weeks since I made the
#RStats
Starter Pack. At the time, Elon had announced blocking rules on X were being changed. I was surprised there wasn't an rstats starter pack here yet, so voila! I added more to it this week, so check it again and follow more.
go.bsky.app/Ki7PjpS
add a skeleton here at some point
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Noe Cochetel
Shelly Gaynor
over 1 year ago
Started a starter pack for botanist!
go.bsky.app/5JTxuk1
add a skeleton here at some point
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Noe Cochetel
Plant Editors
over 1 year ago
Awesome, thanks! Found a few more accounts to add to our starter pack of journals, institutes, and societies! (Welcome
@torreybotanical.bsky.social
and
@plantingscience.bsky.social
).
go.bsky.app/Q9QiX9C
add a skeleton here at some point
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Noe Cochetel
Rob Patro
over 1 year ago
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
add a skeleton here at some point
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Mike Barker
over 1 year ago
I put together a starter pack of people studying plant evolution! I have no doubt missed some folks that should be included, so please reply or message me to be added!
#PlantEvolution
#Botany
go.bsky.app/6FPMYnJ
add a skeleton here at some point
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you reached the end!!
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