NSF Postdoctoral Fellowship in Biology FY 2021: The role of dosage balance in duplicate gene retention

2021 财年 NSF 生物学博士后奖学金：剂量平衡在重复基因保留中的作用

• 批准号: 2109306
• 负责人: Zheng Li
• 金额: $ 13.8万
• 依托单位: Li, Zheng
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2109306&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; FY

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Organisms show immense diversity of lifestyles and forms, and this diversity is based on the origins of new genes during evolution. The main source of new genes is the duplication of older genes. But a central problem is how newly duplicated genes can persist and acquire new functions despite ongoing mutations. Although some duplicate genes are lost quickly, others persist for millions of years. The central hypothesis to explain gene retention is the need to maintain the proper amount of protein products (dosage balance). This dosage balance hypothesis (DBH) has been found to play a major role in gene retention and loss in plants, yeast, and humans. However, it has not been tested in any insects, which represent the majority of animal diversity. This project will address why some duplicate genes are retained over time by testing the DBH in aphids. This project will also shed light on the role of gene duplication, and improve understanding of how genomes evolve. Outreach in bioinformatics and genomics will be conducted in undergraduate biology courses, in addition to the mentoring and training of undergraduate researchers from diverse backgrounds.This project aims to integrate genomics, proteomics, and phenotypic information in aphids to test the DBH as a potential Rule of Life that governs the fate of genes. Aphids are a unique system to test the DBH because they have high fractions of duplicate genes and have not experienced a whole genome duplication. This research will use a comparative genomics approach on chromosome level genome assemblies to reveal the tempo and mode of gene duplications in aphids. This study will also build a protein interaction network using co-fractionation mass spectrometry to determine the interactions of thousands of proteins in aphids, using supervised machine learning. Predictions from the DBH will be tested under a statistical framework by integrating results from gene duplication history and protein interaction networks. This project will also test to determine if DBH can affect ecologically important phenotypes by integrating gene duplication history, with protein interactions, and phenotypic information for gene families with ecological roles involving symbiosis, oxidative stress, and coloration. The Fellow will receive technical training in genomics and proteomics at the University of Texas at Austin. All data and computational resources generated during this project will be freely available to the broader research community through public repositories.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.

这一行动为NSF 2021财年生物学博士后研究奖学金提供了资金，综合研究调查了支配基因组、环境和表型之间相互作用的生命规则。该奖学金支持研究员的研究和培训，这些研究员将以创新的方式为生活规则领域做出贡献。生物体表现出巨大的生活方式和形式的多样性，这种多样性是基于进化过程中新基因的起源。新基因的主要来源是旧基因的复制。但一个核心问题是，尽管不断发生突变，新复制的基因如何能够持续存在并获得新的功能。尽管一些重复的基因很快就消失了，但另一些基因却持续了数百万年。解释基因保留的中心假设是需要维持适量的蛋白质产物(剂量平衡)。这一剂量平衡假说(DBH)已被发现在植物、酵母和人类的基因保留和丢失中发挥着重要作用。然而，它还没有在任何昆虫身上进行测试，这些昆虫代表了大多数动物的多样性。这个项目将通过测试蚜虫的胸径来解决为什么随着时间的推移，一些重复基因会被保留下来。该项目还将阐明基因复制的作用，并提高对基因组如何进化的理解。生物信息学和基因组学的推广将在本科生物学课程中进行，此外还将指导和培训来自不同背景的本科研究人员。该项目旨在整合基因组学、蛋白质组学和表型信息在蚜虫中，以测试胸径作为一种潜在的生命规则来支配基因的命运。蚜虫是测试胸径的独特系统，因为它们有很高比例的重复基因，并且没有经历过全基因组复制。这项研究将使用比较基因组学方法在染色体水平上组装基因组，以揭示蚜虫基因复制的节奏和模式。这项研究还将利用共分馏分质谱建立蛋白质相互作用网络，利用有监督的机器学习来确定数千种蛋白质在蚜虫中的相互作用。通过整合基因复制历史和蛋白质相互作用网络的结果，将在统计框架下测试对胸径的预测。该项目还将进行测试，以确定胸径是否可以通过整合基因复制历史、蛋白质相互作用和具有生态作用的基因家族的表型信息来影响重要的生态表型，这些基因家族涉及共生、氧化应激和着色。这位研究员将在德克萨斯大学奥斯汀分校接受基因组学和蛋白质组学方面的技术培训。项目期间产生的所有数据和计算资源将通过公共资源库免费提供给更广泛的研究社区。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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

Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees

• DOI: 10.1093/gigascience/giad056
• 发表时间: 2023-12-28
• 期刊: GIGASCIENCE
• 影响因子: 9.2
• 作者: Huang，Qiang;Sim，Sheina B.;Evans，Jay D.
• 通讯作者: Evans，Jay D.