Alex Harkess

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

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

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]