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 October 19, 2018


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


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


17) Alex Harkess, Kun Huang, Ron van der Hulst, Bart Tissen, Jeffrey L Caplan, Aakash Koppula, Mona Batish, Blake C Meyers, Jim Leebens-Mack. Sex chromosome evolution via two genes. [biorxiv preprint]

16) One Thousand Plant Transcriptomes Initiative. A Phylogenomic View of Evolutionary Complexity in Green Plants. (in review)

15) Fay-Wei Li, Alex Harkess. A guide to sequencing your favorite plant genome. Applications in Plant Science (2018)[link]

14) Atul Kakrana, Sandra M. Mathioni, Kun Huang, Reza Hammond, Lee Vandivier, Parth Patel, Siwaret Arikit, Olga Shevchenko, Alex E. Harkess, Bruce Kingham, Brian D. Gregory, James H. Leebens- Mack, Blake C. Meyers. Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots Genome Research (2018) [link]

13) Patrick P. Edger, Jocelyn C. Hall, Alex Harkess, Michelle Tang, Jill Coombs, Setareh Mohammadin, M. Eric Schranz, Zhiyong Xiong, James Leebens-Mack, Blake C. Meyers, Kenneth J. Sytsma, Marcus A. Koch, Ihsan A. Al-Shehbaz, and J. Chris Pires. Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses American Journal of Botany (2018) [link]

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. Cell (2018) [link]

11) Alex Harkess et al., The evolution of sex chromosomes in Asparagus. Nature Communications (2017) [link]

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

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