Dimensions US-China: Collaborative Research: Functional Genomics and Experimental Endosymbiont Replacements in Lice.

维度中美：合作研究：虱子的功能基因组学和实验性内共生体替代。

• 批准号: 1926919
• 负责人: Kevin Johnson
• 金额: $ 70.78万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-11-15 至 2024-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1926919&HistoricalAwards=false
• 关键词: Dimensions; US; China; Collaborative; Research

Evolution is a process that optimizes the functions of genes within an organism to facilitate survival in the face of competition and environmental change. While evolution often serves as an engine of invention, it also plays an important role in streamlining, ensuring that organism do not waste resources maintaining or operating superfluous functions. Many animals and plants have evolved symbiotic relationships with microbes in order to gain access to functions that their own genomic inventories do not provide. Microbes participating in these associations experience a dramatic shift from an autonomous lifestyle to one in which their plant or animal host provides many of their needs. Symbiosis provides one of nature's most potent opportunities for evolutionary streamlining, often resulting in the loss of over 90% of ancestral microbial gene functions. This research focuses on understanding the process of evolutionary streamlining in bacterial symbionts of feather-feeding bird lice. These symbioses have evolved (separately) many times from near-identical partners that have colonized different birds but have the same symbiotic functionality. This is a rare and highly prized scenario for the study of an evolutionary process because the high level of repetition provides unique insight into the roles of random change and contingency. This research will also provide a framework for science integration between Chinese and US students and researchers, along with a summer "SIM-biosis" camp that will train 7-9th grade students to develop computer simulations that can decipher the modes and patterns of evolutionary processes. This project focuses on understanding how intimate and interdependent symbiotic relationships originate, function, and co-evolve. While many insects (along with other animals and plants) have evolved symbiotic relationships with bacteria that facilitate the acquisition of important new traits, this project focuses on feather-feeding bird lice, which have repeatedly and independently evolved symbiotic relationships with bacteria to obtain essential B-vitamins that are lacking in their diet of feather keratin. The unusually uniform and simplified lifestyle of these lice presents a unique opportunity to study the evolutionary outcome of repeated acquisition of symbionts under similar conditions. This project explores (i) the role of drift and contingency in shaping the processes of genome evolution and degeneration in symbiotic bacteria, and (ii) the nature and mechanistic basis of integrated functionality. The project uses novel comparative genomic approaches underpinned by machine learning/artificial intelligence algorithms to detect repeating patterns in highly-replicated genomic datasets that effectively represent replays of symbiosis evolution in lice. This will yield highly detailed insight into the molecular evolutionary processes and adaptations that characterize symbiosis and, moreover, the mechanism by which evolution facilitates genomic streamlining in nature.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.

进化是一个优化生物体内基因功能的过程，以促进在竞争和环境变化时的生存。虽然进化通常充当发明的引擎，但它在精简方面也发挥着重要作用，确保有机体不会浪费资源来维持或运行多余的功能。许多动物和植物已经进化出与微生物的共生关系，以获得它们自己的基因组库不提供的功能。参与这些关联的微生物经历了从自主生活方式到植物或动物宿主满足其许多需求的生活方式的巨大转变。共生为自然界提供了最有力的进化精简机会之一，通常会导致 90% 以上的祖先微生物基因功能丧失。 这项研究的重点是了解以羽毛为食的鸟虱细菌共生体的进化精简过程。这些共生体已经从几乎相同的伙伴（分别）进化了很多次，这些伙伴已经殖民了不同的鸟类，但具有相同的共生功能。对于进化过程的研究来说，这是一个罕见且高度珍贵的场景，因为高水平的重复提供了对随机变化和偶然性的作用的独特见解。这项研究还将为中美学生和研究人员之间的科学整合提供一个框架，并举办“SIM-biosis”夏季夏令营，该夏令营将培训 7 至 9 年级的学生开发计算机模拟，以破译进化过程的模式和模式。 该项目的重点是了解亲密且相互依存的共生关系如何起源、发挥作用和共同进化。虽然许多昆虫（以及其他动物和植物）已经进化出与细菌的共生关系，从而有助于获得重要的新性状，但该项目重点关注以羽毛为食的鸟虱，它们反复独立地进化出与细菌的共生关系，以获得必需的 B - 羽毛角蛋白饮食中缺乏的维生素。这些虱子异常统一和简化的生活方式为研究在相似条件下重复获得共生体的进化结果提供了独特的机会。该项目探讨了（i）漂移和偶然性在塑造共生细菌基因组进化和退化过程中的作用，以及（ii）集成功能的本质和机制基础。该项目使用以机器学习/人工智能算法为基础的新颖的比较基因组方法来检测高度复制的基因组数据集中的重复模式，这些重复模式有效地代表了虱子共生进化的重演。这将产生对共生特征的分子进化过程和适应的高度详细的洞察，此外，进化促进自然界基因组精简的机制。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力评估进行评估，被认为值得支持。优点和更广泛的影响审查标准。

项目成果

Mining Ultraconserved Elements From Transcriptome and Genome Data to Explore the Phylogenomics of the Free-living Lice Suborder Psocomorpha (Insecta: Psocodea)

从转录组和基因组数据中挖掘超保守元素，探索自由生活的虱子亚目 Psocomorpha（昆虫纲：Psocodea）的系统基因组学

• DOI: 10.1093/isd/ixac010
• 发表时间: 2022-07
• 期刊: Insect Systematics and Diversity
• 影响因子: 3.4
• 作者: Saenz Manchola, Oscar Fernando;Samacá Sáenz, Ernesto;Virrueta Herrera, Stephany;D’Alessio, Lorenzo Mario;García Aldrete, Alfonso Nerí;Johnson, Kevin P
• 通讯作者: Johnson, Kevin P

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites

鸽子和鸽子的长距离扩散为其寄生虫的宿主转换和适应性辐射创造了新的生态机会

• DOI: 10.1098/rspb.2022.0042
• 发表时间: 2022-03
• 期刊: Proceedings of the Royal Society B: Biological Sciences
• 作者: Boyd, Bret M.;Nguyen, Nam;Allen, Julie M.;Waterhouse, Robert M.;Vo, Kyle B.;Sweet, Andrew D.;Clayton, Dale H.;Bush, Sarah E.;Shapiro, Michael D.;Johnson, Kevin P.
• 通讯作者: Johnson, Kevin P.

The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus

寄主生物地理学和系统发育在羽虱属 Penenirmus 结构多样化中的相互作用

• DOI: 10.1016/j.ympev.2021.107297
• 发表时间: 2021-12
• 期刊: Molecular Phylogenetics and Evolution
• 影响因子: 4.1
• 作者: Johnson, Kevin P.;Weckstein, Jason D.;Virrueta Herrera, Stephany;Doña, Jorge
• 通讯作者: Doña, Jorge

Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice

揭示寄生虱共同进化历史的基因组方法

• DOI: 10.3390/life12091442
• 发表时间: 2022-09
• 期刊: Life
• 作者: Johnson; Kevin P.
• 通讯作者: Kevin P.

The reduced genome of a heritable symbiont from an ectoparasitic feather feeding louse

来自外寄生羽毛食虱的可遗传共生体的基因组减少

• DOI: 10.1186/s12862-021-01840-7
• 发表时间: 2021-12
• 期刊: BMC Ecology and Evolution
• 影响因子: 2.2
• 作者: Alickovic, Leila;Johnson, Kevin P.;Boyd, Bret M.
• 通讯作者: Boyd, Bret M.