MaizeCode - An Initial Analysis of Functional Elements in the Maize Genome

MaizeCode - 玉米基因组功能元素的初步分析

• 批准号: 1445025
• 负责人: Thomas Gingeras
• 金额: $ 591.67万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-15 至 2021-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1445025&HistoricalAwards=false
• 关键词: MaizeCode; Initial; Analysis; Functional; Elements

PI: Thomas Gingeras (Cold Spring Harbor Laboratory)CoPIs: David Jackson, Robert Martienssen, W. Richard McCombie, Michael Schatz, and David Micklos (Cold Spring Harbor Laboratory), Doreen Ware (USDA-ARS/Cold Spring Harbor Laboratory); and Ken Birnbaum (New York University)Maize (corn) is one of the most economically and agriculturally important crops grown in the world. It has assumed this position after centuries of careful genetic breeding to enhance many of its growth and nutritional properties. The generation of high quality genome sequences paired with diverse molecular data allows scientists to better understand the effects of this selective breeding at both the genetic and epigenetic levels. The MaizeCODE project aims to create a comprehensive reference encyclopedia of highly useful genomic reference sequence resources for breeders and plant scientists to use to improve economically important crop traits like disease resistance and yield. In addition, this project will provide broad and comprehensive training opportunities for students, breeders and practicing scientists through specific courses and workshops that will address various approaches to obtain and analyze MaizeCODE data. The Education, Outreach, and Training (EOT) effort will prepare faculty from primarily undergraduate institutions (PUIs) to analyze MaizeCODE with undergraduate students and will provide travel awards for graduate students to attend MaizeCODE training at professional meetings. The EOT program will be unique in promoting Science, Technology, Engineering and Math (STEM) disciplines by anticipating and encouraging broad participation in primary data analysis by undergraduate and graduate students. Improved assemblies of the maize genome will provide a foundation for the identification of biochemically active and biologically functional elements encoded in this working-draft sequence. A comprehensive catalog of these elements will be a critical component in strategies to link genotype with important traits in maize, a classical genetic system. This is the overarching goal of the MaizeCODE project. The human ENCODE project is a model for such a comprehensive catalog. Building on the project team's leadership experience with ENCODE, this similarly integrated and multi-disciplinary project has three main objectives: 1) to develop high-quality working drafts for two inbred maze lines and one teosinte inbred line, 2) to identify regions of the maize genome that are transcribed, methylated, bound by specific modified histones in six cell types that are the major progenitors of the root and shoot systems (focusing on histone modification in three root cell types) and transcription factors in five unrelated tissues and 3) to store, collate, display and disseminate the data to the broader community of plant biologists worldwide. Given the wealth of "genome to phenome" studies in maize, and the emerging realization that much of the variation under selection acts at the level of gene regulation, it is expected that this project will have broad and significant impact on maize genetics research and breeding, with the potential to inform similar research in other grass crops. The project expects to extend significantly the functional annotations and the current understanding of the regulation of gene activity in maize, adding critical content to established databases and graphical genome display centers. Information generated in this project will be rapidly and broadly disseminated using publically available databases and the CyVerse (www.cyverse.org) online resource.

PI：托马斯金格拉斯（冷泉港实验室）CoPI：大卫杰克逊，罗伯特Martienssen，W。Richard McCombie，Michael Schatz，and大卫米克洛斯（冷泉港实验室），Doreen Ware（USDA-ARS/冷泉港实验室）; and Ken Birnbaum（纽约大学）玉米（玉米）是世界上种植的最经济和农业上重要的作物之一。经过几个世纪的精心遗传育种，它已经承担了这一地位，以提高其许多生长和营养特性。高质量基因组序列的产生与多样化的分子数据相结合，使科学家能够更好地了解这种选择性育种在遗传和表观遗传水平上的影响。MaizeCODE项目旨在为育种者和植物科学家创建一个高度有用的基因组参考序列资源的综合参考百科全书，用于改善抗病性和产量等重要的经济作物性状。此外，该项目将通过具体的课程和研讨会为学生、育种者和实践科学家提供广泛和全面的培训机会，这些课程和研讨会将讨论获取和分析玉米编码数据的各种方法。教育，推广和培训（EOT）工作将准备教师主要是本科院校（PUI）与本科生一起分析MaizeCODE，并将为研究生提供旅行奖励，以参加专业会议的MaizeCODE培训。EOT计划将通过预期和鼓励本科生和研究生广泛参与主要数据分析，在促进科学，技术，工程和数学（STEM）学科方面独树一帜。改进的玉米基因组组装将为鉴定该工作草案序列中编码的生物化学活性和生物学功能元件提供基础。 一个全面的目录，这些元素将是一个关键组成部分的战略，以连接基因型与重要性状的玉米，一个经典的遗传系统。这是MaizeCODE项目的首要目标。人类的ENCODE项目就是这样一个综合目录的典范。基于项目团队在ENCODE方面的领导经验，这一类似的综合性多学科项目有三个主要目标：1）为两个近交迷宫系和一个大刍草近交系开发高质量的工作草案，2）鉴定玉米基因组中转录、甲基化，在六种细胞类型中被特定的修饰组蛋白结合，这些细胞类型是根和茎系统的主要祖细胞（关注三种根细胞类型中的组蛋白修饰）和五种不相关组织中的转录因子，以及3）储存，整理，向全世界更广泛的植物生物学家社区展示和传播数据。鉴于玉米“基因组到表型组”研究的丰富性，以及人们逐渐认识到选择作用下的大部分变异作用于基因调控水平，预计该项目将对玉米遗传学研究和育种产生广泛而重大的影响，并有可能为其他禾本科作物的类似研究提供信息。该项目预计将大大扩展功能注释和目前对玉米基因活性调控的理解，为已建立的数据库和图形基因组显示中心添加关键内容。 该项目产生的信息将利用电子数据库和CyVerse（www.cyverse.org）在线资源迅速广泛传播。

项目成果

Sapling: accelerating suffix array queries with learned data models

• DOI: 10.1093/bioinformatics/btaa911
• 发表时间: 2021-03-15
• 期刊: BIOINFORMATICS
• 影响因子: 5.8
• 作者: Kirsche, Melanie;Das, Arun;Schatz, Michael C.
• 通讯作者: Schatz, Michael C.