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

职业：表征植物中雌雄异株的重复进化，以设计人工染色体

• 批准号: 2239530
• 负责人: Alex Harkess
• 金额: $ 159.82万
• 依托单位: HudsonAlpha Institute for Biotechnology
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-01 至 2028-01-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2239530&HistoricalAwards=false
• 关键词: CAREER; Characterizing; repeated; evolution; dioecy

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.

分开的男性和女性个体在生命的许多主要分支中进化，通常是通过独特的染色体对的进化，例如人类的X和Y染色体。这些独特的染色体也存在于一些植物中，并含有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极具挑战性。该项目将为至少100种不同的植物物种生成基因组测序数据，这些植物物种具有单独的雄性和雌性个体，并将特别关注这种独特的染色体，以确定这些控制不同植物雄性和雌性的基因。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如何在植物之间移动来改善植物育种，从而可能增加主要作物物种的产量。在培训和推广方面，这笔赠款将支持一个名为ACTG的计划的扩展：美国校园树基因组，本科生和研究生测序，组装，注释和出版标志性的大学校园树基因组。该项目将在在线教学平台上以多种形式进行教学，例如学期课程和两周短期课程，并向来自全国各地不同大学的学生开放，最终提高进入计算生物学领域的学生的劳动力准备程度。控制雌雄异株的染色体（分开的雄性和雌性个体）在开花植物（被子植物）中已经进化了数百个，如果不是数千个的话。然而，在这些不同的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，部分原因是这些独特的染色体比基因组组装中的常染色体更难以连续组装，这是由于它们在大小和潜在结构变异上的根本差异。该项目采用单基因组方法，使用Illumina测序管道“Cytogenetics-by-Sequencing”来表征至少75个独立的diodeflectin来源，以确定雄性或雌性特异性k-mer的频率，并辨别物种是否具有X/Y或Z/W性染色体。PacBio将为其中至少25个物种生成长读基因组，以组装和完全定相X/Y或Z/W染色体对，鉴定非重组机制（例如倒位，易位，缺失），并鉴定可能控制雄花和雌花发育的基因。这些基因将用于工程化人工染色体（XY或ZW），并通过组装保守的生殖基因的盒并将两性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，来创建新的杂交作物育种系统。该奖项反映了NSF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。

项目成果

A chromosome-scale assembly for ‘d’Anjou’ pear

• DOI: 10.1093/g3journal/jkae003
• 发表时间: 2023-08
• 期刊: G3: Genes|Genomes|Genetics
• 作者: Alan E. Yocca;M. Akinyuwa;Nick P. Bailey;Brannan R Cliver;Harrison Estes;Abigail Guillemette