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

RESEARCH-PGR：活化石：应用单分子测序技术的进步来解码古代植物谱系的大型且复杂的基因组

基本信息

批准号：
1758800
负责人：
William McCombie
金额：
$ 393.62万
依托单位：
Cold Spring Harbor Laboratory
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：
2018-09-01 至 2024-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1758800&HistoricalAwards=false
关键词：
RESEARCH PGR Living Fossils Applying

项目摘要

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.

达尔文首先使用“活化石”一词来描述一组显然完好无损的植物，已有数亿年。在此期间，发生了广泛的环境条件，包括大规模灭绝，但这些植物幸存下来。一个有趣的问题是，活化的化石如何能够在数百万年内持续数百万年，其现存的亲戚如何分歧和进化。这些具有巨大且复杂的基因组的物种属于含有锥体的，非花植物的植物，可以保持理解基因组弹性对环境变化的能力。排序技术的进步现在可以回答这些问题。最近，方法已经可以以合理的成本在遗传上以遗传性来表征这些复杂的生物。这个研究人员的跨学科团队比较了古老，更高度发展的亲戚，以确定基因组的功能，适应和发展的方式。该项目致力于培训下一代科学家，并通过外展活动为公众带来分析和批判性思维能力。在现存的四个裸子谱系中，有三个包含达尔文称为“活化石”的物种。这些自从泥盆纪时代以来就存在，并在各种环境条件下幸存下来。几乎所有裸子植物的基因组都非常大且复杂，因此对基因组表征有些折射。然而，将以合理的成本提供极长的读取（大于10 kb）的牛津纳米孔普罗米特序列序列，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表征。另外，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。将解决有关基因组弹性和进化关系的具体问题。该项目的单分子测序技术的进步将在整个生命科学中产生广泛的影响。教育和宣传计划旨在通过与纽约植物园的参与来提高公众的理解或科学，项目人员将为在美国自然历史博物馆开发展览提供专业知识。所有数据和技术的进步将通过公共存储库公开获得。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评论标准来评估值得支持的。