Research Report 2019_20

Alex Harkess, PhD / Harkess Lab

Investigating genomes across the tree of life

In the spring of 2020, the HudsonAlpha Institute for Biotechnology forged a new collaboration with Auburn University through the addition of a joint research faculty member. Alex Harkess, PhD, joined the Auburn University College of Agriculture as a faculty member in the Department of Crop, Soil and Environmental Scienc- es, and joined HudsonAlpha as a Faculty Investigator. His lab is located on HudsonAlpha’s campus. Prior to his arrival at HudsonAlpha and Auburn, Harkess was a National Science Foundation Postdoctoral Fellow at the Donald Danforth Plant Science Center.




However, about six percent of flowering plants, including asparagus, kiwifruit, and strawberries, have evolved a unique way to reproduce called dioecy. These plants have separate male and female sexes, meaning that flowers will exclusively produce either anthers (male organs) or pistils (female organs). Although dioecy is uncommon, it is predicted to be evolutionarily advantageous because it promotes outcrossing, which increases plant diversity and reduces the expression of harmful mutations from repeated inbreeding. Pinpointing the genetic changes that make a plant male, female, or hermaphrodite is valuable to breeders and growers in order to produce a more robust, durable crop. Wild papaya has an XY chromosome system where- in the presence of a Y chromosome determines a male plant. However, during domestication of papaya, the male Y chromosome was converted to a hermaphrodit- ic Y h so both female and hermaphroditic papaya plants coexist within a population. The reverse transition from male to hermaphrodite is beneficial for inbreed- ing avoidance but the mechanism by which the reversal occurs is not well studied. In a recent study, Harkess and his colleagues sought to identify genes involved in hermaphroditism in papaya by investigating gene ex- pression linked to the X, Y, and Y h chromosomes in pa- paya at different floral developmental stages 1 . The team identified a candidate gene, SHORT VEGETATIVE PHASE (SVG) , associated with both sex determination and the transition to hermaphroditism in papaya. Because plants are stationary organisms, they cannot move away from unfavorable environmental conditions such as changes in climate, pathogens, and herbicides/pesticides. Phenotypic plasticity is a type of

Alex Harkess, PhD

Harkess’s passion lies in the “weird” plants on our planet. His lab uses classical botany and evolutionary biology to look across the tree of life to find cases in which plants have evolved beneficial traits. They also use genetics and genomics to understand which genes are involved in the changes, and translational genomics to engineer those genetic changes into more agricul- turally relevant plants. His research focuses on broad- scale comparative genomics, the evolution and function of small RNA pathways, and the evolution of sex chro- mosomes in plants. Over 90 percent of flowering plants are hermaphro- ditic, meaning that each plant has both male and female reproductive organs and can often reproduce with itself.


HudsonAlpha Institute for Biotechnology

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