NSF Postdoctoral Fellow in Biology at Cornell University
about me
I am a postdoctoral fellow at Cornell University, working with Cedric Feschotte and Ed Buckler.
I graduated from the Population Biology Graduate Group at UC Davis with a PhD in 2019, where I worked with Jeff Ross-Ibarra in the Department of Evolution and Ecology.
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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Experience
2019-present: Postdoctoral fellow, NSF National Plant Genome Initiative, Cornell University
Education
2013-2019: PhD in Population Biology, University of California, Davis
2009: BS in General Biology, University of Washington
2009: BA in Anthropology, University of Washington
Transposable element abundance subtly contributes to lower fitness in maizebiorxiv Michelle C. Stitzer, Merritt Khaipho-Burch, Asher Hudson, Baoxing Song, J. Arcadio Valdez-Franco, Guillaume Ramstein, Cedric Feschotte, Edward Buckler.
Fishing for a reelGene: evaluating gene models with evolution and machine learningbiorxiv
Aimee J Schulz, Jingjing Zhai, Taylor AuBuchon-Elder, Mohamed El-Walid, Taylor H Ferebee, Elizabeth H Gilmore, Matthew B Hufford, Lynn C Johnson, Elizabeth A Kellogg, Thuy La, Evan Long, Zachary R Miller, M Cinta Romay, Arun S. Seetharam, Michelle C Stitzer, Travis Wrightsman, Edward S Buckler, Brandon Monier, Sheng-Kai Hsu.
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansionbiorxiv
Manisha Munasinghe, Andrew Read, Michelle C. Stitzer, Baoxing Song, Claire Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice Hirsch, Nathan Springer.
Two teosintes made modern maizebiorxiv
Ning Yang, Yuebin Wang, Xiangguo Liu, Minliang Jin, Miguel Vallebueno-Estrada, Erin Calfee, Lu Chen, Brian P. Dilkes, Songtao Gui, Xingming Fan, Thomas K. Harper, Douglas J. Kennett, Wenqiang Li, Yanli Lu, Jingyun Luo, Sowmya Mambakkam, Mitra Menon, Samantha Snodgrass, Carl Veller, Shenshen Wu, Siying Wu, Yingjie Xiao, Xiaohong Yang, Michelle C. Stitzer, Daniel Runcie, Jianbing Yan, Jeffrey Ross-Ibarra.
2023
New whole-genome alignment tools are needed for tapping into plant diversityTrends in Plant Science
Baoxing Song, Edward S. Buckler, Michelle C. Stitzer.
2022
AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variationProceedings of the National Academies of Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer.
Controlling for variable transposition rate with an age-adjusted site frequency spectrumGenome Biology and Evolution
Robert Horvath, Mitra Menon, Michelle Stitzer, Jeffrey Ross-Ibarra.
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plantsThe Plant Genome
Yaoyao Wu, Lynn Johnson, Baoxing Song, Cinta Romay, Michelle Stitzer, Adam Siepel, Edward Buckler, Armin Scheben.
Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thalianaNew Phytologist
Alexandre Fournier-Level, Mark A. Taylor, Jefferson F. Paril, Alejandra MartÃnez-Berdeja, Michelle C. Stitzer, Martha D. Cooper, Judith L. Roe, Amity M. Wilczek, Johanna Schmitt.
2021
The genomic ecosystem of transposable elements in maizePLOS Genetics Michelle C. Stitzer, Sarah N. Anderson, Nathan M. Springer, Jeffrey Ross-Ibarra.
Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought toleranceGenome Biology
Xi Wu, Hui Feng, Di Wu, Shijuan Yan, Pei Zhang, Wenbin Wang, Jun Zhang, Junli Ye, Guoxin Dai, Yuan Fan, Weikun Li, Baoxing Song, Zedong Geng, Wanli Yang, Guoxin Chen, Feng Qin, William Terzaghi, Michelle Stitzer, Lin Li, Lizhong Xiong, Jianbing Yan, Edward Buckler, Wanneng Yang, Mingqui Dai.
2020
Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thalianaPNAS
Alejandra Martinez-Berdeja, Michelle C. Stitzer, Mark A. Taylor, Miki Okada, Exequiel Ezcurra, Daniel E. Runcie, Johanna Schmitt.
2019
Transposable elements contribute to dynamic genome content in maizeThe Plant Journal
Sarah N. Anderson, Michelle C. Stitzer, Alex Brohammer, Peng Zhou, Jaclyn M. Noshay, Christine H. O’Connor, Cory D. Hirsch, Jeffrey Ross-Ibarra, Candice N. Hirsch, Nathan M. Springer.
Dynamic patterns of transcript abundance of transposable element families in maizeG3 - Genes|Genomes|Genetics
Sarah N. Anderson, Michelle C. Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D. Hirsch, Nathan M. Springer.
Monitoring the interplay between transposable element families and DNA methylation in maizePLoS Genetics
Jaclyn M. Noshay, Sarah N. Anderson, Peng Zhou, Lexiang Ji, William Ricci, Zefu Lu, Michelle C. Stitzer, Peter A. Crisp, Candice N. Hirsch, Xiaoyu Zhang, Robert J. Schmitz, Nathan M. Springer.
The genome-wide dynamics of purging during selfing in maizeNature Plants
Kyria Roessler, Aline Muyle, Concepcion M. Diez, Garren R.J. Gaut, Alexandros Bousios, Michelle C. Stitzer, Danelle K. Seymour, John F. Doebley, Qingpo Liu, Brandon S. Gaut.
Double triage to identify poorly annotated genes in maize: The missing link in community curationPLoS One
Marcela K. Tello-Ruiz, Cristina F. Marco, Fei-Man Hsu, Rajdeep S. Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C. Barone, Cornel Ghiban, Demitri Muna, Andrew C. Olson, Liya C. Wang, Doreen C. Ware, David A. Micklos.
Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maizeGenetics
Wei Xue, Sarah N. Anderson, Xufeng Wang, Liyan Yang, Peter A. Crisp, Qing Li, Jaclyn Noshay, Patrice S. Albert, James A. Birchler, Paul Bilinski, Michelle C. Stitzer, Jeffrey Ross-Ibarra, Sherry Flint-Garcia, Xuemei Chen, Nathan M. Springer, John F. Doebley.
2018
Maize domestication and gene interactionNew Phytologist Michelle C. Stitzer and Jeffrey Ross-Ibarra.
The maize W22 genome provides a foundation for functional genomics and transposon biologyNature Genetics
Nathan M. Springer, … Michelle C. Stitzer (one of 52 alphabetically listed authors) …, Thomas P. Brutnell.
A kinesin-14 motor activates neocentromeres
to promote meiotic drive in maizeCell
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 differentAmerican 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 technologiesNature
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 StressPLoS Genetics
Irina Makarevitch, Amanda J. Waters, Patrick T. West, Michelle Stitzer, Candice N. Hirsch, Jeffrey Ross-Ibarra, Nathan M. Springer.
Selected Talk, chosen as best student talk: The genomic ecosystem of transposable elements in Zea mays. 2nd Uppsala Transposon Symposium, Uppsala, Sweden, October 4-5, 2018.
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.
Selected Talk: Ecological determinants of transposable element distributions in the B73 maize genome.
58th annual Maize Genetics Conference, Jacksonville, Florida, March 17-20
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:
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.
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.
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.
Fitness costs of transposable elements
TEs are generally thought to be deleterious to host genomes, from both theory and experimental evidence.
Experimental evidence is limited to organisms with small genomes, like yeast and Drosophila.
I am estimating fitness costs by phenotyping maize plants that differ only in TE copy number.
