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

在生命的许多主要分支中，独立的男性和女性个体已经进化出来，通常是通过一对独特染色体的进化，比如人类的X染色体和Y染色体。这些独特的染色体也存在于一些植物中，并包含可以决定植物是雄性还是雌性的基因；然而，这些基因的发现和表征是极具挑战性的。这个项目将产生至少100种不同的植物物种的基因组测序数据，这些物种有单独的雄性和雌性个体，并将特别关注这条独特的染色体，以确定这些基因控制着不同植物的雄性和雌性。这些控制植物雄性和雌性的基因的发现可以通过控制花粉在植物之间的传播来改善植物育种，从而有可能提高主要作物的产量。在培训和推广方面，这笔拨款将支持一个名为ACTG的项目的扩展：美国校园树基因组，由本科生和研究生对标志性的大学校园树基因组进行测序、组装、注释和发布。该课程将在一个在线教学平台上以学期课程和两周短期课程等多种形式授课，并向全国各地不同大学的学生开放，最终提高学生进入计算生物学领域的就业准备。控制雌雄异株（单独的雄性和雌性个体）的染色体在开花植物（被子植物）中独立进化了数百次，如果不是数千次的话。然而，在这些不同的雌雄异株控制染色体上控制雄花和雌花发育的遗传机制仍然难以捉摸，部分原因是由于这些独特的染色体在大小和潜在结构变化方面的根本差异，它们比基因组组装中的常染色体更难以连续组装。该项目采用系统基因组学方法，使用Illumina测序管道“细胞遗传学-测序”来表征至少75个雌雄异株的独立起源，以确定男性或女性特异性k-mers的频率，并辨别一个物种是否具有X/Y或Z/W性染色体。PacBio长读基因组将在至少25个物种中产生，以组装和完全相位X/Y或Z/W染色体对，确定非重组机制（例如倒置，易位，缺失），并确定可能控制雌雄花发育的基因。这些基因将用于设计人工染色体（XY或ZW），并通过组装保守生殖基因的磁带，将雌雄同体物种中的常染色体对功能性地转化为XY和ZW染色体对，形成雌雄异株物种，从而创建一种新的杂交作物育种系统。该提案的广泛影响包括生物信息学、基因组组装和比较基因组学的大规模在线培训机会。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.