CAREER: Characterizing the repeated evolution of dioecy in plants to engineer artificial chromosomes

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Separate male and female individuals have evolved in many major branches of life, often through the evolution of a unique chromosome pair, such as the human X and Y chromosome. These unique chromosomes also exist in some plants and contain genes that can determine whether a plant is male or female; however, these genes are highly challenging to discover and characterize. This project will generate genome sequencing data for at least 100 different plant species that have separate male and female individuals and will focus particularly on this unique chromosome to identify these genes that control maleness and femaleness in diverse plants. The discovery of these genes that control maleness and femaleness in plants can lead to the improvement of plant breeding by controlling how pollen moves from plant to plant, potentially increasing the yield of major crop species. With respect to training and outreach, this grant will support the expansion of a program called ACTG: American Campus Tree Genomes, where undergraduate and graduate students sequence, assemble, annotate, and publish iconic college campus tree genomes. This program will be taught on an online teaching platform in multiple formats, such as semester-long courses and two-week short courses, and open to students from diverse universities around the country, ultimately increasing the workforce readiness of students entering computational biology fields.Chromosomes that control dioecy (separate male and female individuals) have evolved hundreds, if not thousands, of independent times across flowering plants (angiosperms). However, the genetic mechanisms that control male and female flower development on these diverse dioecy controlling chromosomes remain elusive, in part because these unique chromosomes are far more difficult to contiguously assemble than autosomes in genome assemblies due to their fundamental differences in size and potential structure variations. This project takes a phylogenomic approach to characterize at least 75 independent origins of dioecy using an Illumina sequencing pipeline “Cytogenetics-by-Sequencing” to identify the frequency of male or female-specific k-mers and discern if a species has X/Y or Z/W sex chromosomes. PacBio long-read genomes will be generated for at least 25 of those species to assemble and fully phase the X/Y or Z/W chromosome pair, identifying the mechanism of non-recombination (e.g. inversion, translocation, deletion), and identify genes that might control male and female flower development. These genes will be used to engineer artificial chromosomes (XY or ZW) and create a novel hybrid crop breeding system by assembling cassettes of conserved reproductive genes and functionally converting an autosome pair in a hermaphroditic species into an XY and ZW chromosome pair, forming a dioecious species. The broader impacts of this proposal include a large-scale online training opportunity for bioinformatics, genome assembly, and comparative genomics.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.