June

• Mariele Lensink presenting a poster at the Population, Evolutionary, and Quantitative Genetics (PEQG) conference.

May

• The UC Davis Plant Sciences Symposium and the UC Davis EnvironMentors Science Fair are co-hosted on May 1st, 2026! Registration and abstract submissions are now open for the Symposium.

April

• Grey Monroe is co-organizing Mutations in Time and Space at the Wellcome Genome Campus, Cambridge, UK — 13–15 April 2026. Registration is open!
• Matt Davis presenting on somatic mutation diseases in plants and Mariele Lensink presenting on Bayesian methods to infer mutation rate heterogeneity in plant genomes at the conference.

March

• Grey is excited to present his research at UC Riverside — thanks to Sunil K. Kenchanmane Raju for the invitation!

• Congratulations to Kaia Broomell and Alice Pierce, who received a 2026 ROOT & SHOOT Travel Award to attend the American Society of Plant Biologists conference in Ottawa, Canada!

• The full VCF dataset from Zhao et al. is now publicly available via CassavaBase — 1,152 cassava whole-genome sequences representing the most comprehensive centralized compilation of cassava genomic diversity currently available.

• Grey Monroe was promoted to Associate Professor.

• Pablo Luna Rodriguez returned to Peru to complete his undergraduate degree and will continue working with the lab as a remote visiting scholar. We’re excited to continue collaborating!

February

• Congratulations to Evan Long on the acceptance of his paper in BMC Genomics — Protein structure and selection pressure in plants: using mutation to understand the functional importance of protein structure. This work integrates protein structure prediction with population genetics to show that structurally impactful mutations face stronger purifying selection, improving predictions of functional mutation consequences across multiple plant species.

January

• The lab hosted Frank Johannes (TU Munich) for the UC Davis Plant Sciences Seminar Series — his talk covered somatic mutation in trees.
• 

kolibri R package beta version released.

reCYCLing R package beta version released.

• Grey delivered a two-day seminar series at NAIST in Japan on plant genomics and research from the Monroe Lab.

• Welcome Pablo Luna Rodriguez, who joined the Monroe Lab as a visiting scholar from the Universidad Nacional Agraria La Molina in Peru. Pablo is working on haplotype diversity and population genetic analysis in pistachio!

• Grey Monroe organizing the Mutation Workshop at PAG 33 (International Plant and Animal Genome Conference, San Diego, CA, January 9–14) — Friday January 9th at 10AM.

• Kehan Zhao presenting in the Functional Genomics session: Loss of function burden testing for functional gene discovery in plants.

• Chaehee Lee presenting in the Chromosome session: Pistachio superpangenome knobs!

December

• Zhang et al. — Cell layer-specific cell wall modification in pistachio hull splitting · Journal of Experimental Botany — Identifies the specific cell-wall changes that drive the natural hull-splitting phenomenon critical for pistachio harvest.
• Grey presented research at the University College London Department of Genetics, Evolution, and Environment.

November

• Ebrahimi et al. — Phylogenomic analysis of the Juglandaceae reveals black walnut as an ancient lineage · bioRxiv — Comprehensive comparative genomics of the walnut family places black walnut as an evolutionarily ancient and distinct lineage.
• Monroe et al. — Delineating mutation bias and selection during plant development · bioRxiv — Separates the contributions of mutation bias and natural selection in shaping the heritable variant landscape during plant development.
• Welcome Lili Imbler, Erik Spaulding, and Zi Ye, three new undergraduate researchers joining the lab! They will be working on somatic mutation dynamics across diverse plant species.

October

• Pierce et al. — Intron architecture predicts chromatin features in Arabidopsis thaliana · bioRxiv — First intron length and composition predict chromatin state and gene expression levels genome-wide.
• The UC Davis EnvironMentors high school mentorship program is now open for applications — students and mentors can sign up for the 2025–2026 cycle!

September

• Klein et al. — Climate adaptation in Populus trichocarpa: key adaptive loci for stomata and leaf traits · New Phytologist — Identifies genomic loci controlling stomatal and leaf traits relevant to drought adaptation in cottonwood.
• Rose et al. — Introns increase gene expression in C. elegans by a mechanism distinct from plants · Scientific Reports — Intron-mediated enhancement of gene expression operates through partially different mechanisms across kingdoms.

August

• Lensink et al. — Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis · Genetics — Identifies trans-acting loci that control how plants adjust gene expression in response to environmental variation.

July

• Davis et al. — Extreme somatic mutation variation through time and space in walnut clones · bioRxiv — Whole-genome sequencing of walnut clones reveals unexpected heterogeneity in how somatic mutations accumulate across space and developmental time. This work is accompanied by a new haplotype-resolved reference genome for Juglans regia cv. ‘Chandler’ — the most complete walnut genome assembly to date. Raw data and assemblies are publicly available via NCBI BioProject PRJNA1271128 .
• Roy et al. — “The PO-Driven Model”: A Basic Science Pipeline for the Bioeconomy · Integrative and Comparative Biology — A framework using convergent evolution to connect parallel research ideas for bioeconomy applications.

June

• Congratulations to Daniela Quiroz, who successfully defended her Ph.D.! Daniela’s dissertation investigated the role of histone modifications in DNA repair. Her work has been published in The Plant Cell, Current Plant Biology, and more to come. Congratulations, Dr. Quiroz!
• Zhao et al. — Unlocking genetic diversity in Colombian cassava landraces for accelerated breeding · bioRxiv — Characterizes the remarkable genetic diversity among Colombian cassava landraces to accelerate crop improvement.
• Lee et al. — A well-annotated genome of celery (Apium graveolens) with resistance to Fusarium · The Plant Journal — High-quality annotated genome for a disease-resistant celery cultivar, a resource for breeding and functional genomics.
• Congratulations to Alice Pierce, who earned a summer internship at Calico and a DEB Industry Research Fellowship through UC Davis!
• Two UC Davis EnvironMentors students advanced to the GCSE 2025 International Science Fair , held June 16–19 in Chicago alongside the Sustainability Research and Innovation Congress (SRI2025) . Congratulations to Marissa, who won second place nationally for her project on algae monitoring in the UC Davis Arboretum using single-cell fluorescence measurements!

May

• Quiroz et al. — Evolutionary trajectories of cohesin gatekeepers across the Tree of Life · bioRxiv — Traces the deep evolutionary history of cohesin complex regulators from bacteria to plants.
• Grey presented hypotheses on evolutionary drivers of mutation bias at the Evol-Mut-Circle meeting.

April

• Grey co-organized Mutations in Time and Space at the Broad Institute in Cambridge, Massachusetts. Matt Davis presented on somatic mutation accumulation in tissue-cultured walnuts and Satoyo Oya presented on mutation in chromatin-deficient lines in Arabidopsis.
• The Monroe Lab participated in the inaugural UC Davis Environmental Science Fair.

March

• Adaskaveg et al. — In a nutshell: pistachio genome and kernel development · New Phytologist — First high-quality pistachio genome, revealing the genetic basis of kernel development and nutritional quality.

January

• Groh et al. — Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories · Science — Structural variants that arose millions of years ago continue to govern sex-specific reproductive timing across the walnut family.

• Grey hosted the Mutation Workshop at PAG (Plant and Animal Genome Conference). Presentations included:

  • Matt Davis — Somatic mutation in walnut embryos
  • Kehan Zhao — Loss-of-function variation
  • Grey — Chromatin-related mutation drivers in Arabidopsis thaliana
  • Grey — Gene Loss as a Driver of Evolutionary Change and Adaptation (Analysis of Complex Genomes Workshop)
  • Chaehee Lee — Celery genomes for disease resistance discovery and assembly

November

• Alice Pierce and Grey Monroe launch the UC Davis EnvironMentors high school mentorship program.

October

• Matt Davis awarded best presentation at the Bay Area Population Genetics Conference (BAPG)!
• Karasov et al. — Continental-scale associations of Arabidopsis phyllosphere members with host genotype and drought · Nature Microbiology — A continent-wide study showing that host genetics and drought jointly shape the leaf microbiome of wild Arabidopsis.
• Waneka et al. — Gene expression and low-frequency somatic mutations in Arabidopsis via duplex sequencing · Genome Biology and Evolution — Ultra-sensitive duplex sequencing detects rare somatic variants and links their frequency to gene expression patterns.
• Preprint: Monroe et al. — Convergent evolution of epigenome-recruited DNA repair across the Tree of Life · bioRxiv — Shows that directing DNA repair to functionally important regions via the epigenome has evolved independently many times.

September

• Welcome Vianney Ahn, Jr. Specialist joining the lab to work on plant epigenomics!
• Preprint: Klein et al. — Climate adaptation in P. trichocarpa: key adaptive loci for stomata and leaf traits · bioRxiv

July

• Preprint: Adaskaveg et al. — In a nutshell: pistachio genome and kernel development · bioRxiv

June

• Grey and Alice presenting at the American Society of Plant Biologists conference in Honolulu, Hawaii.
• Grey presenting at the Plant Genome Stability and Change Conference in Olomouc, Czech Republic.
• Grey presenting at the Max Planck Institute for Plant Breeding in Cologne, Germany.
• Grey presenting at the East Coast ASPB chapter conference at University of Maryland.

May

• Sutherland et al. — High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features · EMBO Reports — The most diverse immune receptor genes in Arabidopsis share distinctive genomic features including proximity to transposable elements.
• Thanks to Corteva for sponsoring the UC Davis Plant Sciences Symposium !

April

• Grey presenting at Mutations in Time and Space in Edinburgh, Scotland.

March

• Quiroz et al. — H3K4me1 recruits DNA repair proteins in plants · The Plant Cell — The histone mark H3K4me1 directly recruits DNA repair machinery, lowering mutation rates at gene regulatory regions.

January

• Grey, Matt Davis, Chaehee Lee, Evan Long, Kehan Zhao, and Kevin Bird presenting at the Plant and Animal Genome Conference in San Diego.

November

• Welcome Vianney Ahn, undergraduate researcher, to the Monroe Lab!
• Kenchanmane Raju et al. — Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs · New Phytologist — Epigenomic differences between gene duplicates predict their sequence divergence and long-term evolutionary fate.
• Monroe — Are mutations random? · Evolution — Revisits the canonical assumption of mutational randomness, arguing mutation is systematically non-random with respect to genomic function.

October

• Williams et al. — Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants · Genome Biology — Genes with high methylation turnover in their bodies show greater plasticity in expression responses to environmental change.

July

• Monroe et al. — Reply: Re-evaluating evidence for adaptive mutation rate variation · Nature — Responds to critiques of the 2022 findings, reinforcing the evidence for epigenome-modulated mutation rate reduction in plants.
• Welcome Satoyo Oya, HFSP and JSPS Postdoctoral Fellow, to the Monroe Lab!

June

• Welcome Maris Samsel, undergraduate student through the Summer Research Program for Woodland Community College MESA!
• Congratulations to Alice Pierce for a Summer GSR Award for Engineering or Computer-related Applications and Methods!

May

• Congratulations to Mariele Lensink and Matt Davis for receiving full scholarships to attend COMPBIO ASIA 2023 in Singapore!
• Congratulations to Alice Pierce for an ASPB EDIC Recognition Travel Award to present at Plant Biology 2023 in Savannah, Georgia!

April

• Quiroz et al. — Causes of mutation rate variation in plant genomes · Annual Review of Plant Biology — A comprehensive review of the molecular, epigenomic, and evolutionary mechanisms that drive mutation rate variation across plant genomes.
• Grey presenting at the University of Georgia Genetics Department and at the Carnegie Institution for Science at Stanford.
• Mariele Lensink volunteering for IGG science outreach at the UC Davis Picnic Day.

March

• Matt Davis earns Honorable Mention from the NSF Graduate Research Fellowship Program!
• Grey named a finalist for the New Phytologist Tansley Medal for excellence in plant science.
• Monroe et al. — Potential and limits of (mal)adaptive mutation rate plasticity in plants · New Phytologist — Explores scenarios where plasticity in mutation rates could be adaptive or, under some conditions, maladaptive.
• Welcome Megan Lorenc, undergraduate researcher working on pistachio (Pistacia vera) whole-genome sequencing!

February

• Alice Pierce presents her “Journey to Science” at the Young Scholar’s Program Virtual Dinner with a Scientist.

January

• Welcome Evan Long, Postdoctoral Researcher studying pan-genomics of climate adaptation in cassava landraces!

• Matt Davis, Chaehee Lee, and Daniela Quiroz presenting at the Plant and Animal Genome (PAG) conference in San Diego. Grey co-organizes a Mutation workshop at PAG with Ksenia Krasileva.

December

• Grey presenting at the Integrative Plant Epigenetics Cold Spring Harbor Asia conference in Awaji, Japan, and at the University of Tokyo Department of Biological Sciences.

September

• Matt Davis presents at the Corteva Plant Genome Engineering Symposium at UC Berkeley.

August

• Congratulations to Lissandro Ortega for presenting his summer research at the URC Summer Research Symposium!
• Congratulations to Matt Davis for receiving an FFAR Rockey Fellowship for tree nut genomics studies!
• Welcome Kevin Bird, NSF Plant Genome Fellow working on functional genomics of gene network evolution!
• Congratulations to Alice Pierce for receiving a UC Davis Plant Sciences Graduate Research Scholar award!
• Grey presents at the Society for Molecular Biology and Evolution (SMBE) global summit on Mutation Bias and Adaptation.

July

• Congratulations to Daniela Quiroz for receiving a UC Davis Science Translation and Innovative Research (STAIR) grant !

June

• Welcome Lissandro Ortega, undergraduate student in Biochemical Engineering and UC Davis CAMP scholar!
• Welcome Daniela Trippa, visiting scholar working on pistachio genomics!

May

• Preprint: Quiroz et al. — Biased mutagenesis and H3K4me1-targeted DNA repair in plants · bioRxiv
• Grey presents at the annual UC Riverside Institute for Integrative Genome Biology Symposium.
• Alice Pierce outreach at North Bay Science Discovery Day and STEM for Girls at UC Davis.

April

• Grey presents at UC Berkeley Plant and Microbial Biology and at Northwestern University Symposium on Physical Genomics.
• Grey, Matt Davis, and UC Davis graduate students host the 11th annual Corteva Plant Sciences Symposium .

February

• Welcome Chaehee Lee, Postdoctoral Researcher joining the lab to study pan-genomics of pistachio!
• Matt Davis presents at the Texas A&M Plant Breeding Symposium.

January

• Monroe et al. — Mutation bias reflects natural selection in Arabidopsis thaliana · Nature — Landmark study showing mutation rates are systematically lower in functionally important genomic regions, mediated by the epigenome. Featured on NPR Science Friday, the Nature Podcast, and The Scientist.

• Mariele Lensink presents at the Plant and Animal Genome (PAG) conference.

November

• Welcome Daniela Quiroz, PhD candidate in Integrative Genetics and Genomics, to the Monroe Lab!

September

• Welcome rotating PhD students Matt Davis (Plant Biology) and Forrest Li (Integrative Genetics and Genomics)!
• Monroe et al. — Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium · G3 — Combines function-valued trait approaches with quantitative genetics to show how evolutionary constraints shift across a soil moisture gradient.

August

• Congratulations to Kehan Zhao for passing his Qualifying Exam!
• Congratulations to Kehan Zhao for receiving a UC Davis Plant Sciences Graduate Research Scholar award!

June

• Mariele Lensink, Kehan Zhao, and Grey present research at Evolution 2021.
• Welcome Sydney Wren, undergraduate research assistant!

May

• Welcome Camryn Morey, undergraduate intern!
• Congratulations to Kehan Zhao and Mariele Lensink for Plant Sciences Graduate Student Researcher Fellowship awards!

April

• Welcome Andrea Moron-Solano, undergraduate student!
• Lab awarded a HiFi sequencing grant by PacBio to study climate adaptation in pistachio.

March

• Welcome Kehan Zhao, Plant Biology PhD student studying the evolutionary significance of loss-of-function mutations in climate adaptation!
• Mariele Lensink and Elton Kane officially join the lab.
• Grey and co-author Pádraic Flood interviewed by the Heredity Podcast about our paper on adaptive loss of function.

February

• Monroe et al. — Genomics of adaptive loss of function in plants · Heredity — Shows that loss-of-function mutations are disproportionately represented among variants underlying climate adaptation in Arabidopsis.
• We are recruiting for multiple funded positions — prospective postdocs interested in plant genomics are encouraged to get in touch!

January

• Welcome Ian Anderson, research intern studying mutation bias remotely!

• Welcome Lea Berg, visiting scholar developing bioinformatic pipelines for functional genomic variation in crop wild relatives!

• Welcome Elton Kane, rotating Plant Biology student developing robot-powered high-throughput genotyping methods!

• Welcome Alissza Ali, undergraduate student studying phenotypic variation in natural populations across climate gradients!

October

• Welcome Harrison Yu, undergraduate student working on computational approaches to studying mutation bias across the tree of life!
• Monroe et al. — The role of beneficial loss-of-function mutations in crop evolution · Current Plant Biology — Documents how beneficial knockout mutations have contributed to the evolution of key crop traits through domestication and breeding.
• Lab event: Catalyzing Adaptive and Resilient Food Systems — Over 300 participants from around the world discussing sustainable agriculture in the face of climate change, sponsored by the UC Davis World Food Center.

July

• Baggs et al. — Convergent loss of an EDS1/PAD4 signaling pathway reveals coevolved immunity and drought response · The Plant Cell — Multiple plant lineages independently lost a key immunity pathway, revealing a surprising evolutionary link between disease resistance and drought tolerance.

• Monroe et al. preprint on mutation bias in Arabidopsis thaliana featured on PreLights and Plantae .

• The Monroe Lab officially opens at UC Davis! 🌱