RESEARCH-PGR: Living Fossils: Applying advances in single molecule sequencing to decode large and complex genomes of ancient plant lineages

达尔文首次使用“活化石”一词来描述一组显然已经完整地存活了数亿年的植物。 在此期间，发生了各种各样的环境条件，包括大规模的灭绝，但这些植物存活了下来。一个有趣的问题是，活化石如何能够持续数百万年，以及它们现存的亲戚如何分化和进化。这些物种属于结球果、不开花的植物，称为裸子植物，它们具有巨大而复杂的基因组，可以为理解基因组对环境变化的适应性提供线索。测序技术的进步现在可以回答这些问题。 最近，已经有方法可以以合理的成本从基因上表征这些复杂的生物体。这个跨学科的研究团队比较了古代和更高度进化的亲属，以确定基因组如何发挥作用，适应和进化。该项目致力于培训下一代科学家，并通过外联活动向公众传授分析和批判性思维技能。 在现存的四个裸子植物谱系中，有三个包含被达尔文称为“活化石”的物种。“这些自泥盆纪以来就存在，并在一系列令人难以置信的环境条件下幸存下来。几乎所有裸子植物的基因组都非常庞大和复杂，因此对基因组特征的研究有些困难。 然而，Oxford Nanopore PromethION测序仪的开发，可以以合理的成本提供极长的读取（大于10 kb），将用于对这些植物的基因组及其更现代的辐射谱系进行详细表征。此外，将从多个组织中分析这些物种的甲基化状态，以了解表观基因组变异性。关于基因组弹性和进化关系的具体问题将得到解决。该项目在单分子测序技术方面的进展将对整个生命科学产生广泛的影响。教育和外联方案旨在通过与纽约植物园的合作提高公众对科学的理解，项目人员将为美国自然历史博物馆的展品开发提供专业知识。所有数据和技术进步将通过公共存储库公开提供。该奖项反映了NSF的法定使命，并被认为值得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来支持。

Darwin first used the term "living fossils" to describe a group of plants that had apparently survived intact for hundreds of millions of years. During this time a wide range of environmental conditions occurred, including mass extinctions, and yet these plants survived. An intriguing question is how the living fossils were able to persist over millions of years and further, how their extant relatives diverged and evolved. Belonging to the cone-bearing, non-flowering group of plants, called gymnosperms, these species with huge and complex genomes could hold clues to understanding genomic resilience to environmental change. Advances in sequencing technologies are now available to answer these questions. Very recently, approaches have become available to characterize these complex organisms genetically at a reasonable cost. This interdisciplinary team of researchers compare ancient and more highly evolved relatives to identify how genomes function, adapt and evolve. The project is dedicated to training the next generation of scientists and brings analytical and critical thinking skills to the general public through outreach activities. Three of the four extant gymnosperm lineages contain species which Darwin termed "living fossils." These have been present since the Devonian Era and have survived an incredible range of environmental conditions. The genomes of almost all the gymnosperms are extremely large and complex and have been somewhat refractive to genomic characterization as a result. However, the development of the Oxford Nanopore PromethION sequencer, which can provide extremely long reads (greater than 10 kb) at a reasonable cost, will be used to carry out detailed characterization of the genomes of these plants as well as their more modern, radiated lineages. In addition, the methylation status of these species will be analyzed from multiple tissues to understand epigenomic variability. Specific questions about genome resilience and evolutionary relationships will be addressed. Advances in single molecule sequencing technologies from this project will have broad impact across the life sciences. Educational and outreach programs are designed to improve public understanding or science through engagement with the New York Botanical Garden, and project personnel will contribute expertise to developing exhibits at the American Museum of Natural History. All data and technology advances will be publicly available 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.