about me

I am a graduate student in the Population Biology Graduate Group at UC Davis, in Jeff Ross-Ibarra’s lab in the Department of Plant Sciences.

I am interested in the evolutionary forces acting on and enacted by transposable elements in plant genomes. Most of my work involves the genus Zea, which includes maize and wild relatives collectively called teosintes. Transposable elements were first discovered in maize, due to the dramatic and unexpected spots and speckles they caused on kernels when they jumped in and out of anthocyanin genes during development. Although the extent of transposable elements was unknown upon their discovery, now, DNA derived from transposable elements is known to make up 85% of the maize genome. How do these exceptional mutagens persist? What forms of regulation and cooperation have evolved between transposon and host? Between different kinds of transposable elements? How can knowledge of these interactions be leveraged in agricultural systems?

For more detailed questions, please see my research page.

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Education

2013-present: PhD student, Population Biology Graduate Group, University of California, Davis
2009: BS in General Biology, University of Washington
2009: BA in Anthropology, University of Washington

Publications

Preprints

Maize domestication and gene interaction PeerJ Preprints
Michelle C. Stitzer and Jeffrey Ross-Ibarra.

2018

A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize Cell
R. Kelly Dawe, Elizabeth G. Lowry, Jonathan I. Gent, Michelle C. Stitzer, Kyle W. Swentowsky, David M. Higgins, Jeffrey Ross-Ibarra, Jason G. Wallace, Lisa B. Kanizay, Magdy Alabady, Weihong Qiu, Kuo-Fu Tseng, Na Wang, Zhi Gao, James A. Birchler, Alex E. Harkess, Amy L. Hodges, Evelyn N. Hiatt.

Adaptation in plant genomes: bigger is different American Journal of Botany
Wenbin Mei, Markus G. Stetter, Daniel J. Gates, Michelle C. Stitzer, Jeffrey Ross-Ibarra.

2017

The complex sequence landscape of maize revealed by single molecule technologies Nature
Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael May, Nathan Springer, Eric Antoniou, Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R. Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware.

2015

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress PLoS Genetics
Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle Stitzer, Candice N. Hirsch, Jeffrey Ross-Ibarra, Nathan M. Springer.

Recent Presentations

Upcoming

Selected Talk: Selection against LTR retrotransposons is balanced by locally adapted transposable element alleles in Arabidopsis thaliana.
Population, Evolutionary and Quantitative Genetics Conference, Madison, WI, May 13-16, 2018.

Selected Talk: Ecological determinants of transposable element survival in Zea mays.
Evolution, 2nd Joint Congress on Evolutionary Biology, Montpellier, France, August 19-22, 2018.

2018

Poster: Atypical transposable elements predict functional consequence.
60th Annual Maize Genetics Conference, St. Malo, France, March 22-25, 2018.

Talk: Validation of structural annotation of genes and transposable elements in maize.
Plant and Animal Genome XXVI, San Diego, California, January 13 - 17.

2017

Selected Talk: Ecological determinants of transposable element survival in Zea mays.
Plant Genomes and Biotechnology: From Genes to Networks, Cold Spring Harbor Laboratory, New York, November 29 - December 2.

Talk: Transposable elements in Arabidopsis thaliana - Population genetics of TE polymorphism.
Bay Area Population Genomics, Stanford, California, November 4.

Selected Talk: Selection against LTR retrotransposons is balanced by locally adapted transposable element alleles in Arabidopsis thaliana.
The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements, EMBL Heidelberg, Germany, October 11-14.

Selected Talk: Selection against LTR retrotransposons is balanced by locally adapted transposable element alleles in Arabidosis thaliana.
Hamilton Award Finalist Evolution 2017, Portland, Oregon, June 23-27.

Invited talk: Diverse ecological strategies allow transposable element survival in the maize genome.
University of Georgia Plant Center Spring Symposium, Athens, Georgia, May 9.

Talk: Genome assembly of a heterozygous teosinte: Zea diploperennis.
Maize genomes workshop, 59th annual Maize Genetics Conference, St Louis, Missouri, March 9.

2016

Talk: Evolutionary dynamics of transposable elements in Zea mays.
Center for Population Biology Seminar Series, Davis, California, April 5.

Selected Talk: Ecological determinants of transposable element distributions in the B73 maize genome.
58th annual Maize Genetics Conference, Jacksonville, Florida, March 17-20

Awards

2017

ARCS - Achievement Rewards for College Scientists, Eileen D. and Lisa C. Ludwig Endowment Fund Scholar

2016

Jastro Shields Research Grant, UC Davis Center for Population Biology

ARCS - Achievement Rewards for College Scientists, Eileen D. and Lisa C. Ludwig Endowment Fund Scholar

2015

CPB Research Award, UC Davis Center for Population Biology

2014

Global Food Initiative Fellowship - Lawrence Berkeley National Laboratory and University of California Office of the President

2013

National Science Foundation Graduate Research Fellowship

Teaching

Fall 2014 & 2016, Teaching Assistant for BIS101 Introductory Genetics, UC Davis

research

My research is driven by an interest in how transposable elements (TEs) interact with their host genome.

Specifically, I focus on:

  1. Transposable element annotation in complex genomes, retaining information about recently transposed copies.
    • The majority of the maize genome consists of tranpsosable elements, so a newly arriving transposable element is most likely to land in an existing transposon copy in the genome.
    • I developed methods to reconstruct these past transposition events, and have applied this approach to recover 130,000 intact transposon copies in the maize inbred line B73 AGPv4 assembly.
    • An annotation of this scale predicates work on identifying polymorphism between individual genotypes, and the impact of TEs on gene expression, methylation, and general genome regulation.
  2. The ecology of the genome.
    • Transposable elements can be envisioned as species within an ecosystem of genomic space, with composition dictated by both their own features and their host genome.
    • I am applying community ecology approaches to understand the genomic features that allow survival of TE families through time.
    • While many biologists consider transposable elements to have similar functions, in large genomes like maize, individual TE families have evolved dramatically different niche preferences to evade their host.
    • Understanding these niches allows prioritization and prediction of TE insertions that are likely mutagenic, such as when they occur in regions of the genome that differs from their genomic niche.
  3. Signatures of selection on transposable elements, as generated by sequence divergence after transposition.
    • Several adaptive traits in maize are due to tranpsosable element insertions, such as the Hopscotch TE insertion 80kb upstream of tb1, which is fixed in all maize, and restricts lateral branching.
    • I am applying population genetic methods to detect selection on TE sequences, by comparing nucleotide substitutions within individual TE loci to their allele frequency.
    • Although theory predicts TEs will be on average slightly deleterious to their host, the distribution of these effects is largely uninvestigated in plants.
    • I am applying these approaches in Arabidopsis thaliana, maize, and the teosinte Zea mays subsp. parviglumis.
  4. The role of transposable element polymorphism in gene regulation.
    • Plant genomes often methylate TE sequences, which restricts their transcriptional and therefore transpositional abilities.
    • Sometimes, this methylation spreads into adjacent sequences, or the presence of a TE changes the local chromatin state.
    • I am using TE polymorphism data to disentangle cause and effect of TEs that target chromosomal regions, or are removed by natural selection after insertion.
    • Understanding the impact of new TE insertions on gene expression and regulation will allow greater prediction of phenotype, and prioritization of candidate mutants for further research.