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”一词来描述一组似乎完好无损地存活了数亿年的植物。在这段时间里，各种各样的环境条件发生了变化，包括大灭绝，但这些植物却存活了下来。一个有趣的问题是，这些活化石是如何能够存活数百万年甚至更长时间的，它们现存的亲戚是如何分化和进化的。这些具有巨大而复杂基因组的物种属于不开花的植物裸子植物，它们可以为理解基因组对环境变化的适应能力提供线索。测序技术的进步现在可以回答这些问题。最近，已经有一些方法可以用合理的成本来描述这些复杂生物体的遗传特征。这个跨学科的研究小组比较了古代和高度进化的亲属，以确定基因组是如何功能、适应和进化的。该项目致力于培养下一代科学家，并通过外展活动向公众传授分析和批判性思维技能。现存的四种裸子植物谱系中有三种包含达尔文称之为“活化石”的物种。它们从泥盆纪就存在了，在各种环境条件下都存活了下来。几乎所有裸子植物的基因组都是非常大和复杂的，因此在基因组表征方面有些屈光。然而，牛津纳米孔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以及它们更现代的辐射谱系进行详细的表征。此外，将从多个组织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被解决。单分子测序技术的进步将对整个生命科学产生广泛的影响。教育和推广计划旨在通过与纽约植物园的接触来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览提供专业知识。所有的数据和技术进步都将通过公共存储库公开提供。该奖项反映了美国国家科学基金会的法定使命，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。

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.