Monroe Lab @ UC Davis
Plant genomics on a changing planet
We study genetic variation in plants at the intersection of molecular biology, evolutionary theory, and functional genomics.
--What's new?---
January 2024
Grey, Matt Davis, Chaehee Lee, Evan Long, Kehan Zhao, and Kevin Bird are all presenting at Plant and Animal Genome Conference in San Diego.
November 2023
Welcome Vianney Ahn, undergraduate researcher, to the Monroe lab!
Paper: Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs
October 2023
July 2023
Paper: Reply to: Re-evaluating evidence for adaptive mutation rate variation
Welcome Satoyo Oya, HFSP and JSPS Postdoctoral fellow to the Monroe lab!
June 2023
Welcome Maris Samsel, undergraduate student through the Summer Research Program for Woodland Community College MESA!
Congrats Alice for receiving a Summer GSR Award for Engineering or Computer-related Applications and Methods!
May 2023
Congratulations to Mariele and Matt for receiving full scholarships to attend COMPBIO ASIA 23 JULY 9-22 2023 in SINGAPORE !
Congratulations to Alice for receiving a Recognition Travel Award from the Equity, Diversity and Inclusion Committee (EDIC) of the American Society of Plant Biologists (ASPB) to present here research at Plant Biology 2023 - August 5 – 9 | Savannah, Georgia!
April 2023
Paper! Causes of Mutation Rate Variation in Plant Genomes. Annual Reviews in Plant Biology
Alice participates in Science Fair Day at the Library at the Mary L. Stephens Davis Library showcasing plant anatomical diversity
Grey presenting at the University of Georgia Genetics Department.
Grey presenting at the Carnegie Institution for Science @ Stanford University.
Mariele Lensink volunteering for IGG science outreach event at the annual UC Davis Picnic Day. Transgenic fish! (Now beloved lab pets)
March 2023
Alice participates at North Bay Science Discovery Day to teach children how to extract DNA from strawberries, presents a poster at the UC Davis Biotechnology retreat, and receives a honorable mention on the National Academy of Sciences Ford Foundation Fellowship!
Matt earns Honorable Mention from NSF GRFP!
Grey was a finalist for the New Phytologist Tansley Medal for excellence in plant science :) https://www.newphytologist.org/news/view/324, associated paper below:
Paper! Potential and limits of (mal)adaptive mutation rate plasticity in plants. New Phytologist
Preprint! Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in A. thaliana. biorXiv
Welcome Undergraduate student Megan Lorenc who is joining the lab to help generate whole genome sequence datasets in Pistacia vera.
February 2023
Alice presents about her “Journey to Science” at the Young Scholar’s Program Virtual Dinner with a Scientist
January 2023
Welcome to Postdoctoral Researcher Evan Long, who will be studying pan-genomics of climate adaptation in landraces of cassava!
Matt, Chaehee, and Daniela presenting at Plant and Animal Genome (PAG) conference in San Diego. Grey is organizing Mutation workshop at PAG together with Ksenia Krasileva.
December 2022
Grey presenting at the Integrative Plant Epigenetics Cold Spring Harbor Asia conference in Awaji Japan and the Department of Biological Sciences at the University of Toyko
Preprint! Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity. biorXiv
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:
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 positions - Prospective 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!
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.