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.

单独的男性和女性个体在生活的许多主要分支中经常进化，通常是通过独特的染色体对的演变，例如人X和Y染色体。这些独特的染色体也存在于某些植物中，并包含可以确定植物是雄性还是雌性的基因。但是，这些基因的发现和表征高度挑战。该项目将生成至少有100种具有单独男性个体的植物物种的基因组测序数据，并特别关注这种独特的染色体，以识别控制潜水员植物中男性和女性的这些基因。通过控制花粉如何从植物到植物移动，可能会提高主要农作物的产量，从而发现控制植物中男性和女性的这些基因可以改善植物育种。关于培训和外展，该赠款将支持一个名为ACTG：美国校园树基因组的计划，本科生和研究生序列，组装，注释和发布标志性的大学校园树基因组。该课程将以多种格式的在线教学平台上教授，例如学期的课程和为期两周的短课程，并向来自全国各地大学大学的学生开放，最终增加了进入计算生物学领域的学生的劳动力准备。然而，控制这些潜水染色体的雄性和女性花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在基因组组件中的常染色体组装的难度要难以连续，因为它们的大小和潜在结构变化。该项目采用系统切开术方法来表征至少75个独立的二元起源，并使用Illumina测序管道“按后期的细胞遗传学”来识别男性或女性特异性K-Mers的频率，并识别物种是否具有X/Y或Z/W w seles selmosomes。 PACBIO长阅读基因组将至少为其中25种，以组装和完全相位X/Y或Z/W染色体对，从而识别非重组的机制（例如，反转，易位，缺失，缺失），并识别可能控制雄性和女性花发展的基因。这些基因将用于设计人造染色体（XY或ZW），并通过组装保守的生殖基因的盒子来创建一种新型的杂化作物育种系统，并在功能上将雌雄同体中的自染色体对转化为XY和ZW染色体对，形成了鸡蛋，形成了鸡蛋。该提案的更广泛影响包括针对生物信息学，基因组议会和比较基因组学的大规模在线培训机会。该奖项反映了NSF的法定任务，并被认为是通过基金会的智力优点和更广泛的影响来通过评估来获得的支持。

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

Complementing model species with model clades

• DOI: 10.1093/plcell/koad260
• 发表时间: 2023-10-12
• 期刊: PLANT CELL
• 影响因子: 11.6
• 作者: Mabry，Makenzie E.;Abrahams，R. Shawn;Harkess，Alex E.
• 通讯作者: Harkess，Alex E.