About Me

  • 2007-2011

    Miami University

    B.S. Botany, Environmental Science

    I spent four years as an undergraduate in Richard Moore's lab studying population genetics of X/Y gene pairs in dioecious papaya

  • 2011-2016

    University of Georgia

    Ph.D, Plant Biology

    I completed my PhD working with Jim Leebens-Mack studying sex chromosomes, polyploidy, phylogenomics, transposon dynamics, big genome assembly and annotation, and a general interest in the evolution of sex

  • 2016-present

    Donald Danforth Plant Science Center

    NSF Plant Genome Initiative Postdoctoral Fellow

    I am currently working with Blake Meyers on comparative genomics and small RNA evolution across the land plants, with a particular focus on Dicer-like proteins, Argonautes, and 21 and 24nt reproductive phasiRNAs



  • Curriculum Vitae

    Click asparagus for CV
    Updated April 27, 2017

Research

My interests are broad, but encompass skills learned in the lab, the greenhouse, and at the terminal

I also believe in open science and a commitment to code sharing. See my github account.



Sex Chromosomes

I am using a suite of reverse genetic, sequencing, and bioinformatic strategies to identify gender determination genes on the garden asparagus Y chromosome

Polyploidy

Whole genome duplications have run amok in the flowering plants. I enjoy taking syntenic and phylogenomic approaches with genome and transcriptome data to identify these events in big trees.

Basal Angiosperms

The basal angiosperms are a particularly special group of angiosperms. I am especially interested in Amborella trichopoda and the Nymphaeales waterlilies, which both exhibit a variety of sexual diversity.



Small RNAs

Small RNAs are processed and function in myriad unique ways in plants. I am currently studying how gene and genome duplications have influenced Dicer-like protein evolution in the monocots, and its associated role in phasiRNA biogenesis

Plant-Fungal interactions

A peculiar fungal parasitism can convert Silene latifolia XX females into hermaphrodites. I am identifying the mechanisms plant-fungal molecule exchange and the evolutionary arms race between these two species



Short on time? Here are my finalist competition videos for the 3 Minute Thesis competition during graduate school at UGA


2014 - Top 10 Finalist


2015 - 2nd Place

Publications



12) R. Kelly Dawe, Elizabeth G. Lowry, Jonathan I. Gent, Michelle C. Stitzer, David M. Higgins, Lisa B. Kanizay, Jeffrey Ross-Ibarra, Magdy Alabady, Na Wang, Alex E. Harkess, Amy L. Hodges, Evelyn N. Hiatt. Kinesin-driven neocentromeres promote meiotic drive in maize. (in review)


11) Alex Harkess et al., The evolution of sex chromosomes in Asparagus. (in review)


10) Alex Harkess, Jim Leebens-Mack. A century of sex determination in plants. Heredity (2017) [link]


9) Dieter Hackenberg, Michael R. McKain, Soon Goo Lee, Tyler McCann, Spencer Schreier, Alex Harkess, J. Chris Pires, Gane Ka-Shu Wong, Joseph M. Jez, Elizabeth Kellogg and Sona Pandey. Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytologist (2016) [link]


8) Richard Moore, Alex Harkess, Laura Weingartner. How to be a seXY plant model: a holistic view of sex-chromosome research. American Journal of Botany (2016) [link]


7) Alex Harkess, Francesco Mercati, Francesco Sunseri, J. Chris Pires, Agostino Falavigna, Jim Leebens-Mack. Retrotransposon expansion coincident with the evolution of dioecy and sex chromosomes in Asparagus. G3: Genes, Genomes, Genetics (2016) [link] [Dryad]


6) Ray Ming, Robert Van Buren ... Alex Harkess, Michael Mckain ... Qingyi Yu. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics (2015). [link]


5) Alex Harkess, Francesco Mercati, Francesco Sunseri, Agostino Falavigna, Jim Leebens-Mack. Sex-biased gene expression in dioecious garden asparagus. New Phytologist (2015). [SRA] [Dryad] [link]


4) Steven B. Cannon*, Michael McKain*, Alex Harkess*, Matthew Nelson, Sudhansu Dash, Michael Deyholos, Neil Stewart, Yanhui Peng, Blake Joyce, Charles N. Stewart Jr., Megan Rolf, Toni Kutchan, Xuemei Tan, Cui Chen, Yong Zhang, Eric Carpenter, Gane Ka-Shu Wong, Jeff J. Doyle, Jim Leebens-Mack. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Molecular Biology and Evolution (2015). * = equal contributors. [Dryad] [link]


3) Francesco Mercati, Paolo Riccardi, Alex Harkess, Tea Sala, Maria Rosa Abenavoli, Jim Leebens-Mack, Agostino Falavigna, Francesco Sunseri. SNP-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification. Molecular Breeding (2015) [link]


2) Amborella Genome Project. The Amborella Genome and the Evolution of Flowering Plants. Science (2013) [link]


1) Jonathan I Gent, Nathanael I Ellis, Lin Guo, Alex E. Harkess, Yingyin Yao, Xiaoyu Zhang, R. Kelly Dawe. CHH Islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Research (2012) [link]


Publications in preparation

Contact Me

using the links below