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.

入侵物种威胁生物多样性，影响作物，重建生态系统，促进疾病，破坏基础设施，每年造成1200亿美元的损失。尽管有这些影响，但对引入物种如何以及为什么会成为入侵物种的理解是惊人的不完整。这种知识差距反映了缺乏有关入侵早期阶段和进化在促进入侵中的作用的信息。最近基因组测序和计算技术的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植物标本馆标本的基因组序列，研究人员能够及时后退，并检查从最初引入到现在促进入侵的模式和过程。植物入侵基因组学联盟（CPING）将利用这场基因组革命产生的大数据来研究入侵物种，并培养一代科学家掌握新的基因组方法。通过合作项目集中在五个国家关注的入侵物种，CPING最初设在路易斯安那大学拉斐特分校，南达科他州州立大学，亚拉巴马大学，塔斯卡卢萨，西弗吉尼亚大学，和威奇托州立大学将扩大到联合科学家和学生在60多个机构在18个EPSCoR国家，以更好地了解植物如何成为入侵，并提供见解，管理和预防入侵物种。CPING包括一个为各级学术界（本科生到教师）设计的新基因组学方法培训计划，包括为期5天的基因组学训练营，将培训来自区域和当地学院和大学的36名科学家。所有参与者将为五个CPING重点物种的项目做出贡献，并在自己的实验室进行个人研究项目，为39名本科生提供动手研究的机会。通过结合来自许多EPSCoR管辖区的科学家的专业知识和资源，CPING将促进植物入侵的高度合作调查，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STEM教育。尽管对入侵物种的研究和控制进行了大量投资，由于缺乏大多数入侵植物的基因组资源，关于入侵性的遗传基础和进化的基本问题仍然知之甚少。该项目最初汇集了来自路易斯安那大学拉斐特分校、南达科他州州立大学、亚拉巴马大学塔斯卡卢萨分校、西弗吉尼亚大学和威奇托州立大学的科学家，成立了植物入侵基因组学联盟（CPING），该联盟将EPSCoR机构的教师联合起来，研究殖民化、基因流动和适应如何塑造种群动态，并促进五种备受瞩目的入侵物种的入侵。对于每个重点物种，CPING参与者将对当代和历史标本应用尖端方法，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几个长期存在的关于入侵的问题：1）殖民动态-数量，位置，时间和遗传多样性-如何影响物种在新环境中的建立和传播？(2)杂交会影响侵袭性吗？(3)适应是否导致基因组和表型的新奇，可能促进入侵？总之，五个CPING重点项目将产生一个新的，综合的理解，参与入侵植物的传播的关键种群水平的过程中的作用，以及提供物种特异性的见解的重要性无性繁殖，多倍体，和基因组结构的入侵。CPING的一个平行重点是建立一个由具有基因组学和生物信息学知识的科学家组成的合作网络，这些科学家能够将入侵物种作为国家关注的问题加以解决。CPING将采用轴辐式组织结构，在超过18个EPSCoR司法管辖区的机构培训教师和学生。对参与者的直接好处包括扩大他们的研究能力，提高他们对资金的竞争力，并提高他们提供基因组学和生物信息学教育的能力。CPING培训研讨会将产生丰富的公开提供的培训教程，实验室协议和教材。CPING还计划通过当地广播节目和与研究人员的互动，让公众参与入侵物种的问题和预防。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

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

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

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.

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.