Reference Annotations for Small RNA-producing Genes in Plants

PI: Michael J. Axtell（宾夕法尼亚州立大学-大学公园）CoPI: Matthew Jones-Rhoades（诺克斯学院）基因是染色体内编码特定功能产物的DNA的离散部分。基因表达是这些离散DNA片段的RNA拷贝的产生，这些片段要么用来编码蛋白质，要么作为RNA本身的功能。基因注释在整个完整的基因组序列中识别和表征基因的位置。蛋白质编码基因的注释受到了极大的关注，并且对于许多具有农业和经济利益的植物物种来说，蛋白质编码基因的注释处于相对先进的状态。相比之下，许多其他类型的基因的注释就不那么发达了。调控小RNA是一种短片段RNA，其功能是关闭基因组中其他基因的表达，并在几种重要的植物性状中起关键作用，包括抗病性、对不利环境条件的耐受性和影响产量的植物生长性状。调控小RNA基因的一个亚型，即microrna，已经得到了很好的研究和注释。然而，microRNAs只占植物小RNA基因总数的很小一部分；初步数据表明，一个典型的植物基因组只有几百个microRNA基因，但是有成千上万的基因编码其他类型的调节小rna。该项目旨在为几种具有农业和社会意义的植物，包括水稻、玉米、番茄和苹果，提供产生所有类型的调控小rna的植物基因的系统注释。了解基因在基因组中的位置，以及它们产生的产品类型，是植物遗传改良方法的关键信息。调节性小rna显然是植物中主要的基因类型，但其注释目前还不发达。对调控小RNA基因进行系统、可靠的基因注释，将加速遗传、基因组和育种实验，以确定优良的植物品种，以应对在气候变化的情况下养活不断增长的人口和保持美国农业惊人的生产力的挑战。该项目还通过指导的研究经验培养现代植物遗传学的研究生和本科生，并允许开发新的本科课程。本项目的所有成果将不受限制地通过项目网站http://plantsmallrnagenes.psu.edu/提供。序列数据将通过长期存储库（GEO， SRA）提供，小RNA基因模型将提供给Gramene和MaizeGDB等社区门户网站。

PI: Michael J. Axtell (Pennsylvania State University - University Park)CoPI: Matthew Jones-Rhoades (Knox College)Genes are discrete sections of DNA within chromosomes that encode specific functional products. Gene expression is the production of RNA copies of these discrete DNA sections that are then either used to encode for proteins, or are functional as RNAs in their own right. Gene annotations identify and characterize the location of genes throughout a complete genome sequence. Annotations of protein-coding genes have received a great deal of attention, and are at a relatively advanced state for many plant species of agricultural and economic interest. In contrast, annotations for many other types of genes are much less developed. Regulatory small RNAs are short bits of RNA that function to turn off the expression of other genes in the genome and have been implicated as key players in several important plant traits, including disease resistance, tolerance to adverse environmental conditions, and plant growth traits affecting yield. One sub-type of regulatory small RNA genes, the microRNAs, are well-studied and well-annotated. However, microRNAs account for a very small fraction of the overall small RNA gene population in plants; preliminary data indicate that a typical plant genome has just a few hundred microRNA genes, but tens of thousands of genes encoding other types of regulatory small RNAs. This project seeks to provide systematic annotations of plant genes that produce all types regulatory small RNAs for several plants of agricultural and societal interest, including rice, maize, tomato, and apple.Knowing where in the genome the genes are, and what types of products they produce, is key information for genetic approaches to plant improvement. Regulatory small RNAs are clearly a major type of gene in plants, but their annotation is currently under-developed. Systematic and reliable gene annotations for regulatory small RNA genes will accelerate genetic, genomic, and breeding experiments to identify superior plant varieties to meet the challenge of feeding a growing population and maintaining the astounding productivity of American agriculture in the face of a changing climate. This project is also training graduate and undergraduate students in modern plant genetics through mentored research experience, and allowing the development of novel undergraduate courses. All project outcomes from this project will be made available without restriction via the project website at http://plantsmallrnagenes.psu.edu/. Sequence data will be available through long-term repositories (GEO, SRA) and small RNA gene models will be provided to community portals such as Gramene and MaizeGDB.