Plant genomics on a changing planet

We study genetic variation in plants at the intersection of evolutionary theory, functional population genomics, and molecular biology.

--What's new?---

September 2022

Alice Pierce volunteers at the AvenueB Transfer Bridge Networking eventNetwork with incoming undergraduate underrepresented transfer students from the College of Biological Sciences at UC Davis to expose them to different career paths and education opportunities after college

 

Matt Davis presents at Corteva Plant Genome Engineering Symposium 2022 at UC Berkeley

August 2022

Lissandro Ortega presented his summer research at the URC's Summer Research Symposium!

Congrats to Matt Davis for receiving an FFAR Rockey Fellowship!

https://www.plantsciences.ucdavis.edu/news/davis-lands-rockey-fellowship-tree-nut-studies

 

Welcome, Kevin Bird, NSF Plant Genome Fellow working on the functional genomics of gene network evolution with our lab and Dan Kliebenstein!

Congrats to Alice Pierce for recieving a UC Davis Plant Sciences Graduate Research Scholar award!

Grey presents at the Society for Molecular Biology and Evolution global summit on Mutation Bias and Adaptation.

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

Preprint online: https://www.biorxiv.org/content/10.1101/2022.08.21.504682v1 

July 2022

Congrats to Daniela for recievng a UC Davis Science Translation and Innovative Research (STAIR) program grant.

https://www.plantsciences.ucdavis.edu/news/monroe-quiroz-seek-way-speed-genome-research​

 

June 2022

Welcome, Lissandro Ortega, undergraduate student in Biochemical Engineering and UC Davis CAMP scholar!

Welcome Daniela Trippa, visiting scholar working on Pistachio genomics!

 

May 2022

Alice Pierce spends a day of outreach at the North Bay Science Discovery Day, teaching kids how to do DNA extractions :) Alice also led microscopy demonstrations at STEM for girls sponsored by the Women’s Resources and Research Center at UC Davis!

Grey presents at annual UC Riverside Institute for Integrative Genome Biology Symposium.

Biased mutagenesis and H3K4me1-targeted DNA repair in plants
Preprint from Daniela Quiroz et al online: https://www.biorxiv.org/content/10.1101/2022.05.28.493846v2

 

April 2022

Alice Pierce volunteers at the UC Davis Picnic Day for the Science Communication club at UC Davis

 

Grey presents at UC Berkeley Department Plant and Microbial Biology.

Grey presents at Northwestern University 2022 Symposium on Physical Genomics.

 

Grey, Matt Davis and a group of UC Davis graduate students host the 11th annual Corteva Plant Sciences Symposium

http://plantsciencesymposium.ucdavis.edu/. Also there were awesome posters by Daniela Quiroz, Alice Pierce and Chaehee Lee!

 

February 2022

Matt Davis presents at Texas A&M Plant Breeding Symposium.

 

Welcome, Chaehee Lee, a Postdoctoral Researcher who is joining our lab to study pan-genomics of Pistachio!

Alice volunteers at Women & Girls in STEM at Explorit, with Hands-on activities geared towards children to promote scientific career paths for young women, with a focus on Plant Biology/Botany literacy.

January 2022

Matt Davis presents at American Seed Trade Association Vegetable & Flower Seed Conference.

 

Mariele Lensink presents at Plant and Animal Genome conference.

 

Paper "Mutation bias reflects natural selection in Arabidopsis thaliana" published in Nature! Here we find evidence that Arabidopsis has a significant reduction in mutation rate in functionally conserved regions of the genome, and evidence that this is mediated by the epigenome. Accompanied by a nice News & Views by Jianzhi Zhang. 

 

To help understand where this work relates to documented ideas about mutation, we've written a short document On Mutational Randomness, a survey of the view that mutations are random with respect to consequences. 

Paper Featured on:

NPR Science Friday

Nature Podcast

The Scientist
 

November 2021

Welcome, Daniela Quiroz, PhD candidate in Integrative Genetics and Genomics who is joining our lab!

 

September 2021

Welcome to rotating PhD students Matt Davis from Plant Biology and Forrest Li from Integrative Genetics and Genomics!

Paper "Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium" published! Here we combined function-valued trait approaches with quantitative genetic estimates of evolutionary constraint to ask "how do evolutionary constraints change as a function of water availability?"

Book review of "Evolutionary Genetics: Concepts, Analysis, and Practice by Glenn-Peter Sætre and Mark Ravinet" now online. tldr; its a great book! 

August 2021

Congrats to Kehan for passing his Qualifying Exam!

And Congrats to Kehan for recieving a UC Davis Plant Sciences Graduate Research Scholar award!

July 2021

New Postdoc position open: Postdoctoral Researcher in Pan-Genomics

June 2021

Mariele, Kehan, and Grey present recent research at Evolution 2021.

Welcome to undergraduate research assistant Sydney Wren!

 

May 2021

Welcome to undergraduate intern Camyrn Morey!

 

Congrats to Kehan and Mariele for Plant Sciences Graduate Student Researcher Fellowship awards!

 

April 2021

Welcome to undergraduate student Andrea Moron-Solano!

Our international team is awarded HiFi sequencing grant by PacBio to study climate adaptation in Pistachio. Blog post here.

March 2021

Welcome to Kehan Zhao, Plant Biology Ph.D. student who will be investigating the evolutionary significance of natural loss-of-function mutations during climate adaptation!

Mariele (co-advised with Dan Kliebenstein) and Elton (co-advised with Christine Diepenbrock) officially join our lab!

Grey and co-author Pádraic Flood ​interviewed by Heredity Podcast about our recent paper

February 2021

Our paper on the genomics of adaptive loss of function is published!

 

We are recruiting for multiple funded positionsProspective postdocs interested in plant genomics are encouraged to get in touch!​

Welcome to rotating Integrative Genetics and Genomics student Mariele Lensink who will be examining the evolutionary consequences of transcription-related mutation!

January 2021

 

Our preprint on Brachypodium responses to soil moisture gradient earns a recommendation from PCI Evolutionary Biology's Benoit Pujol: https://evolbiol.peercommunityin.org/public/rec?id=231.

 

Welcome to research intern Ian Anderson, volunteering in the lab remotely to study mutation bias!

Welcome to visiting scholar Lea Berg, developing bioinformatic pipelines to investigate functional genomic variation crop wild relatives!

Welcome to Elton Kane, a rotating student from the Plant Biology Graduate Group working on developing robot-powered high throughput genotyping methods!

Welcome to Alissza Ali, an undergraduate student looking at phenotypic variation in natural populations adapted across diverse climate gradients!

 

October 2020

 

Welcome to Harrison Yu, an undergraduate student working on computational approaches to studying mutation bias across the tree of life!

Paper on the role of beneficial knockout mutations in crop evolution published!

Our event Catalyzing Adaptive and Resilient Food Systems sponsored by the UC Davis World Food Center and Air Quality Research Center, organized through the Climate Adaptation Research Center was a huge success - over 300 people tuned in from around the world to hear from industry leaders, policymakers, and researchers about developing sustainable agricultural systems in the face of climate change. Looking forward to more events to come. Most of the talks are recorded and can be found on the event page.

July 2020

Collaboration with Erin Baggs, Ksenia Krasileva, et al. published in Plant Cell "Convergent loss of an EDS1/PAD4 signaling pathway in several plant lineages reveals coevolved components of plant immunity and drought response"

 

Our recent preprint on mutation bias in Arabidopsis thaliana gets featured by Facundo Romani at PreLights and Caroline Dowling at Plantae! 

Monroe (The Genomics of Climate Adaptation) Lab officially opens its doors at UC Davis! 

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UC Davis Land Acknowledgement Statement:

We should take a moment to acknowledge the land on which we are gathered. For thousands of years, this land has been the home of Patwin people. Today, there are three federally recognized Patwin tribes: Cachil DeHe Band of Wintun Indians of the Colusa Indian Community, Kletsel Dehe Wintun Nation, and Yocha Dehe Wintun Nation.

The Patwin people have remained committed to the stewardship of this land over many centuries. It has been cherished and protected, as elders have instructed the young through generations. We are honored and grateful to be here today on their traditional lands.