Collaborative Research: Diversity of Physcomitrium pyriforme in North America and Europe: significance of autopolyploidy within a phylogenomic and experimental framework

合作研究：北美和欧洲梨形小须藻的多样性：系统发育和实验框架内同源多倍体的重要性

• 批准号: 1753800
• 负责人: Matthew Johnson
• 金额: $ 41.77万
• 依托单位: Texas Tech University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1753800&HistoricalAwards=false
• 关键词: Collaborative; Research; Diversity; Physcomitrium; pyriforme

This project will investigate the effects of genome duplication in plants. Many plant species, including some agricultural crops, have arisen as a result of genome duplication. This natural event results in offspring having genomes that are doubled in content or more as compared to their parents and may have provided opportunities for innovation during plant evolution. However, the short- and long-term consequences of genome duplication in wild plants are not well understood. This research will investigate the natural rate of genome duplication in a wild moss species distributed in North America and Europe. Researchers will create experimental, genome-duplicated offspring in the laboratory to measure how their morphology and reproduction differs from that of their parents. They will then determine if and how duplicated genomes may change over time by comparing the experimental, genome-duplicated offspring to those that occur naturally. Researchers will train undergraduate and graduate students, including members of under-represented groups, and support the professional development of early-career researchers. They will also host regional outreach lectures for K-12 teachers about best-practices in evolutionary biology education. Researchers will engage the public online using the citizen-science iNaturalist platform and will create bilingual (Spanish/English) blog posts about moss biology and polyploid evolution. This project will expand our understanding of the consequences of autopolyploid evolution in plants. Researchers will use as an experimental model organism the moss species Physcomitrium pyriforme (Funariaceae, the Funaria moss family), which harbors a morphologically-diverse complex of seven karyotypes worldwide. The species is annual, bisexual, selfing, and is easily grown in the laboratory. Unlike most other plant model organisms, its genome content can be doubled with precision in vitro to create autopolyploid offspring. Researchers will compare reproductive barriers among naturally-occurring and artificially-induced autopolyploids as well as their homoploid progenitors. Project outcomes will include a phylogeny of the Physcomitrium pyriforme species-complex based on genome sequence data, an estimate of ploidy changes within the complex over evolutionary time and among populations today, and the description of new species. Researchers will further develop the HybPiper bioinformatics data analysis platform and train other US scientists in this method to enhance research capacity. The project will strengthen research collaborations among US institutions and build natural-history collections.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.

该项目将研究基因组重复对植物的影响。许多植物物种，包括一些农作物，由于基因组复制而引起了。与父母相比，这种自然事件导致后代的基因组在含量或更大的含义上增加了一倍，并且可能在植物进化过程中提供了创新的机会。但是，野生植物中基因组重复的短期和长期后果尚不清楚。这项研究将调查在北美和欧洲分布的野生苔藓物种中基因组重复的自然率。研究人员将在实验室中创建实验性，基因组赋予的后代，以衡量其形态和繁殖与父母的形态和生殖如何不同。然后，他们将通过将实验，基因组赋予的后代与自然发生的后代进行比较，并确定重复的基因组是否会随时间变化。研究人员将培训本科生和研究生，包括代表性不足的群体的成员，并支持早期研究人员的专业发展。他们还将为K-12教师举办有关进化生物学教育最佳实践的区域外展讲座。研究人员将使用Citizen-Science Inaturalist平台在线参与公众，并将创建有关Moss生物学和多倍体进化的双语（西班牙语/英语）博客文章。该项目将扩大我们对植物自身多倍体演化后果的理解。研究人员将用作实验模型生物，苔藓物种Phymcomitrium pyrimare（Funariaceae，Funaria Moss家族），它具有全球七种核型的形态多样性复合体。该物种是一年一度的，双性恋的，自我的，在实验室中很容易生长。与大多数其他植物模型生物不同，其基因组含量可以在体外精确地加倍以创建自动多倍体后代。研究人员将比较自然存在和人为诱导的自身聚集体及其同型祖细胞的生殖障碍。项目结果将包括基于基因组序列数据的Pyrimorte物种复合物的系统发育，对复合物内部和当今种群中的倍数变化的估计以及对新物种的描述。研究人员将进一步开发Hybpiper生物信息学数据分析平台，并以这种方法培训其他美国科学家来增强研究能力。该项目将加强美国机构之间的研究合作，并建立自然历史集合。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评估标准，被认为值得通过评估来获得支持。

项目成果

Phylogenomics resolves the rediscovered Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), as a species of Entosthodon , prompting also the transfer of Clavitheca poeltii

系统基因组学解析了重新发现的喜马拉雅特有的 Brachymeniopsis gynostoma（苔藓植物，Funariaceae），作为 Entosthodon 的一种，也促进了 Clavitheca poeltii 的转移

• DOI: 10.1002/tax.13106
• 发表时间: 2023
• 期刊: TAXON
• 影响因子: 3.4
• 作者: Zhang, Li;Zuo, Qin;Ma, Wen‐Zhang;Shevock, James R.;Patel, Nikisha;Johnson, Matthew;Medina, Rafael;Wilding, Nicholas;Goffinet, Bernard
• 通讯作者: Goffinet, Bernard

Vindication of Physcomitrium pygmaeum (Funariaceae), an elusive and endangered moss from North America's Great Basin

Physcomitrium pygmaeum（葫芦科）的辩护，这是一种来自北美大盆地的难以捉摸的濒临灭绝的苔藓

• DOI: 10.1639/0007-2745-125.4.528
• 发表时间: 2022
• 期刊: The Bryologist
• 作者: Medina, Rafael;Johnson, Matthew G.;Patel, Nikisha;Tocci, Genevieve E.;Toren, David R.;Goffinet, Bernard
• 通讯作者: Goffinet, Bernard

Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

通过目标核基因的亚基因组定相鉴定出苔藓属 Physcomitrium 和 Entosthodon (Funariaceae) 中远缘祖先的频繁异源多倍体

• DOI: 10.1093/evolut/qpad171
• 发表时间: 2023
• 期刊: Evolution
• 影响因子: 3.3
• 作者: Patel, Nikisha;Medina, Rafael;Williams, Lindsay D.;Lemieux, Olivia;Goffinet, Bernard;Johnson, Matthew G.;Betancourt, ed., Andrea;Chapman, ed., Tracey
• 通讯作者: Chapman, ed., Tracey

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

• DOI: 10.1111/2041-210x.14072
• 发表时间: 2023-03-13
• 期刊: METHODS IN ECOLOGY AND EVOLUTION
• 影响因子: 6.6
• 作者: Freyman, William A.;Johnson, Matthew G.;Rothfels, Carl J.
• 通讯作者: Rothfels, Carl J.