Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

合作研究：RoL：出芽酵母基因型-表型图谱的演变

• 批准号: 2110404
• 负责人: Antonis Rokas
• 金额: $ 95万
• 依托单位: Vanderbilt University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-15 至 2026-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2110404&HistoricalAwards=false
• 关键词: Collaborative; Research; RoL; Evolution; Genotype

How organisms’ external characteristics or traits are encoded in their genomes and how they change over time represent important and largely unanswered biological questions. This project will address these questions by studying the metabolisms and genomes of the more than 1,000 known species of budding yeasts and their evolution. Some of these yeast species are important opportunistic pathogens, while others are of great industrial relevance as producers of foods, beverages, medicines, and biofuels. This project will span multiple scales of biological organization (from molecules to cells, species, and beyond) and ~400 million years of evolution to yield fundamental insights into how traits are encoded in genomes, how new functions evolve, and how the relationship between traits and genomes itself evolves. The project will support the Wild YEAST and Computational Genomics Programs, two established and highly successful educational and training programs that immerse early-stage undergraduate students, including those from underrepresented backgrounds, in authentic, discovery-driven research.Using draft genomes for nearly all known budding yeast species and state-of-the-art genome-editing tools that are broadly active in diverse species, this project will predict the connection of every metabolic gene in every yeast species’ genome to its function(s), as well as examine the evolution of every known metabolic gene, pathway, and trait across the budding yeast subphylum Saccharomycotina. Through genome-scale evolutionary analyses and targeted functional experiments on key representative taxa spanning budding yeast genomic and metabolic diversity, this project will functionally characterize how between-taxa variation at the level of genotypes gives rise to variation at the level of phenotypes. In particular, the project will chart how variation at the level of DNA, RNA, proteins, and metabolites sequentially transforms genetic variation into biochemical functions and physiological traits with an emphasis on functionally characterizing gaps and correcting discrepancies in the predicted Genotype-Phenotype Map.This project is jointly funded by the Evolutionary Processes program in the Division of Environmental Biology and the Genetic Mechanisms program in the Division of Molecular and Cellular Biosciences of the Directorate for Biological Sciences.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.

生物体的外部特征或性状如何在其基因组中编码，以及它们如何随时间变化，这些都是重要的、基本上尚未回答的生物学问题。该项目将通过研究1,000多种已知芽殖酵母的代谢和基因组及其进化来解决这些问题。这些酵母菌中的一些是重要的机会致病菌，而另一些则作为食品，饮料，药品和生物燃料的生产商具有很大的工业相关性。该项目将跨越生物组织的多个尺度（从分子到细胞，物种等）和约4亿年的进化，以获得关于性状如何在基因组中编码，新功能如何进化以及性状与基因组之间的关系如何进化的基本见解。该项目将支持野生酵母和计算基因组学计划，这两个已经建立并非常成功的教育和培训计划，使早期的本科生，包括那些来自代表性不足的背景的学生，沉浸在真实的，以发现为导向的研究中。使用几乎所有已知的芽殖酵母物种的基因组草案和在不同物种中广泛活跃的最先进的基因组编辑工具，这个计划将预测每一种酵母基因组中的每一个代谢基因与其功能的联系，以及研究每一个已知的代谢基因、途径和性状在芽生酵母亚门中的进化。通过对跨越芽殖酵母基因组和代谢多样性的关键代表性分类群进行基因组规模的进化分析和有针对性的功能实验，该项目将在功能上表征基因型水平上的分类群间变异如何引起表型水平上的变异。特别是，该项目将绘制DNA，RNA，蛋白质，和代谢物依次将遗传变异转化为生化功能和生理性状，重点是功能上表征差距和纠正预测基因型中的差异，表型图。该项目由环境生物学系的进化过程项目和遗传机制项目共同资助。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

BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data

BioKIT：用于处理和分析不同类型序列数据的多功能工具包

• DOI: 10.1093/genetics/iyac079
• 发表时间: 2022
• 期刊: Genetics
• 影响因子: 3.3
• 作者: Steenwyk, Jacob L;Buida, Thomas J;Gonçalves, Carla;Goltz, Dayna C;Morales, Grace;Mead, Matthew E;LaBella, Abigail L;Chavez, Christina M;Schmitz, Jonathan E;Hadjifrangiskou, Maria
• 通讯作者: Hadjifrangiskou, Maria

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

• DOI: 10.3114/sim.2023.105.01
• 发表时间: 2023-06-01
• 期刊: STUDIES IN MYCOLOGY
• 影响因子: 16.5
• 作者: Groenewald，M.;Hittinger，C. T.;Rokas，A.
• 通讯作者: Rokas，A.

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum

• DOI: 10.1016/j.cub.2022.10.025
• 发表时间: 2022-12-19
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: Li, Yuanning;Liu, Hongyue;Rokas, Antonis
• 通讯作者: Rokas, Antonis