RII Track-2 FEC: Consortium for Plant Invasion Genomics (CPING): Combining Big Data and Plant Collections to Understand Invasiveness

RII Track-2 FEC：植物入侵基因组学联盟 (CPING)：结合大数据和植物收集来了解入侵性

• 批准号: 1920858
• 负责人: Nicholas Kooyers
• 金额: $ 383.55万
• 依托单位: University of Louisiana at Lafayette
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1920858&HistoricalAwards=false
• 关键词: RII; Track; FEC; Consortium; Plant

Invasive species threaten biodiversity, impact crops, restructure ecosystems, promote disease, and damage infrastructure, costing the US $120 billion annually. Despite these impacts, understanding of how and why introduced species become invasive is shockingly incomplete. This knowledge gap reflects a lack of information about the early stages of invasions and the role of evolution in promoting invasiveness. The recent revolution in genome sequencing and computing technology promises to narrow this gap. By comparing genome sequences of historic herbarium specimens spanning the duration of an invasion, researchers are able to step back in time and examine the patterns and processes that promote invasion from initial introduction to present day. The Consortium for Plant INvasion Genomics (CPING) will harness the Big Data generated by this genomic revolution for the study of invasive species and train a generation of scientists in new genomic methods. Through collaborative projects focused on five invasive species of national concern, CPING initially housed at the University of Louisiana at Lafayette, South Dakota State University, the University of Alabama, Tuscaloosa, West Virginia University, and Wichita State University will expand to unite scientists and students at more than 60 institutions in 18 EPSCoR states to better understand how plants become invasive and provide insights into the management and prevention of invasive species. CPING incorporates a training program in new genomic methods designed for all levels of academia (undergraduate students to faculty) comprising 5-day genomics bootcamps that will train 36 scientists from regional and local colleges and universities. All participants will contribute to projects on the five CPING focal species and conduct individual research projects in their own labs, providing hands-on research opportunities for 39 undergraduate students. By combining expertise and resources from scientists across many EPSCoR jurisdictions, CPING will facilitate highly collaborative investigation of plant invasions, provide training in key genomic techniques, enable EPSCoR researchers to better compete for funding, and foster genomics and bioinformatics STEM education.Despite immense investment into the study and control of invasive species, fundamental questions regarding the genetic basis and evolution of invasiveness remain poorly understood due to a lack of genomic resources for most invasive plants. The project initially brings together scientists from the University of Louisiana at Lafayette, South Dakota State University, the University of Alabama, Tuscaloosa, West Virginia University, and Wichita State University to form the Consortium for Plant INvasion Genomics (CPING) unites faculty across EPSCoR institutions to examine how colonization, gene flow, and adaptation shape population dynamics and facilitate invasion in five high-profile invasive species. For each focal species, CPING participants will apply cutting-edge methods to contemporary and historical specimens to build spatial and temporal genomic datasets spanning entire invasions. We will harness this Big Data to address several long-standing questions regarding invasions: 1) How do colonization dynamics-the number, location, timing, and genetic diversity-impact the establishment and spread of species in new environments? (2) Does hybridization impact invasiveness? (3) Does adaptation lead to genomic and phenotypic novelty that may facilitate invasion? Together, the five CPING focal projects will yield a novel, synthetic understanding of the roles of the crucial population-level processes involved in the spread of invasive plants, as well as offer species-specific insights on the importance of asexuality, polyploidy, and genome structure in invasiveness. A parallel focus of CPING is building a collaborative network of genomics and bioinformatics literate scientists capable of addressing invasive species as a problem of national concern. CPING will employ a hub-and-spoke organizational structure to train faculty and students at institutions in more than 18 EPSCoR jurisdictions. Direct benefits to participants include expanding their research capabilities, increasing their competitiveness for funding, and improving their ability to provide genomics and bioinformatics education. CPING training workshops will produce a wealth of publicly available training tutorials, laboratory protocols, and teaching materials. CPING also plans to engage the public on the problem and prevention of invasive species through local radio programming and interactions with researchers.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.

入侵物种威胁着生物多样性，影响作物，重组生态系统，促进疾病和损害基础设施，每年耗资1200亿美元。尽管有这些影响，但了解引入物种的侵入性如何以及为什么是令人震惊的不完整。这种知识差距反映出缺乏有关入侵早期阶段的信息以及进化在促进侵入性中的作用。基因组测序和计算技术的最近革命有望缩小这一差距。通过比较跨越入侵持续时间的历史标本室标本的基因组序列，研究人员能够退后一步，并检查从最初介绍到当今的最初介绍的模式和过程。植物入侵基因组学联盟（CPING）将利用这一基因组革命对入侵物种的研究产生的大数据，并以新的基因组方法培训一代科学家。通过合作项目的重点关注五种具有入侵性的国家关注，CPing最初安置在路易斯安那大学拉斐特大学，南达科他州立大学，阿拉巴马大学，托斯卡卢萨大学，西弗吉尼亚大学和威奇托州立大学将在18个epscor的企业中融合到60多个机构中，并将成为欧普斯特州的60多个机构，并将 物种。 Cping将培训计划纳入了针对所有级别的学术界（本科生到教师）设计的新基因组方法的培训计划，该方法包括为期5天的基因组学训练营，该训练训练营将培训来自地区和地方学院和大学的36位科学家。所有参与者将为五个CPASE焦点物种的项目做出贡献，并在自己的实验室中进行单个研究项目，为39名本科生提供动手研究机会。通过将科学家的专业知识和资源结合在一起，CPing将促进对植物入侵的高度协作调查，提供关键基因组技术的培训，使Epscor研究人员能够更好地竞争资金，并促进基因组学和生物信息学的贫困依据，以对贫困的研究和投资进行研究。由于缺乏大多数侵入性植物的基因组资源而理解。该项目最初将路易斯安那大学拉斐特大学的科学家汇集在一起入侵物种。对于每个焦点物种，CPAING参与者将向当代和历史标本应用最先进的方法，以构建跨越整个入侵的空间和时间基因组数据集。我们将利用这些大数据来解决有关入侵的几个长期问题：1）殖民动态如何 - 数量，位置，时间和遗传多样性影响新环境中物种的建立和传播？ （2）杂交会影响侵入性吗？ （3）适应是否会导致可能促进入侵的基因组和表型新颖性？总之，五个CPANE焦点项目将产生对涉及侵入性植物传播的关键种群过程的作用的新颖，合成的理解，并提供有关与无性，多倍体和基因组结构在侵入性中的重要性的特定物种特定见解。 CPING的一个平行重点是建立一个基因组学和生物信息学识字科学家的协作网络，能够解决入侵物种作为国家关注的问题。 Cping将采用轮毂和辐条的组织结构来培训超过18个EPSCOR司法管辖区的机构的教职员工和学生。对参与者的直接好处包括扩大其研究能力，提高其资金竞争力，以及提高其提供基因组学和生物信息学教育的能力。 Cping培训研讨会将制作大量公开可用的培训教程，实验室协议和教材。 Cping还计划通过本地无线电节目和与研究人员的互动与公众有关入侵物种的问题和预防。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响审查标准，认为值得通过评估来获得支持。

项目成果

Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome

• DOI: 10.1128/aem.00744-21
• 发表时间: 2021-08-01
• 期刊: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 4.4
• 作者: Paudel, Santosh;Bagale, Kamal;Kulkarni, Ritwij
• 通讯作者: Kulkarni, Ritwij

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

• DOI: 10.7717/peerj.9315
• 发表时间: 2020-06-16
• 期刊: PEERJ
• 影响因子: 2.7
• 作者: Barrett, Craig F.

Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum.

• DOI: 10.1002/ajb2.1852
• 发表时间: 2022-05
• 期刊: AMERICAN JOURNAL OF BOTANY
• 影响因子: 3
• 作者: Barrett, Craig F.;Huebner, Cynthia D.;Bender, Zoe A.;Budinsky, Trezalka A.;Corbett, Cameron W.;Latvis, Maribeth;McKain, Michael R.;Motley, M'Kayla;Skibicki, Samuel V.;Thixton, Hana L.;Santee, Mathilda V.;Cumberledge, Aubrey N.
• 通讯作者: Cumberledge, Aubrey N.

Genetic, morphological, and niche variation in the widely hybridizing Rhus integrifolia‐Rhus ovata species complex

广泛杂交的大叶漆树-卵形漆树物种复合体的遗传、形态和生态位变异

• DOI: 10.1111/1442-1984.12293
• 发表时间: 2021
• 期刊: Plant Species Biology
• 影响因子: 1.4
• 作者: Barrett, Craig F.;Lambert, Joshua;Santee, Mathilda V.;Sinn, Brandon T.;Skibicki, Samuel V.;Stephens, Heather M.;Thixton, Hana
• 通讯作者: Thixton, Hana

The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower

普通猴花植物防御权衡的遗传结构

• DOI: 10.1093/jhered/esaa015
• 发表时间: 2020
• 期刊: Journal of Heredity
• 影响因子: 3.1
• 作者: Kooyers, Nicholas J;Donofrio, Abigail;Blackman, Benjamin K;Holeski, Liza M;Hodges, Scott
• 通讯作者: Hodges, Scott