Comparative Genomics of a Species Radiation: Sequencing the Apple Tribe

物种辐射的比较基因组学：对苹果部落进行测序

• 批准号: 1416825
• 负责人: Elena Kramer
• 金额: $ 30万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-01-15 至 2016-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1416825&HistoricalAwards=false
• 关键词: Comparative; Genomics; Species; Radiation; Sequencing

PI: Sarah Mathews (Harvard University)Key Collaborator: Erin MacNeal Rehrig (Fitchburg State University)Species radiations are a striking feature of evolution and may be responsible for much of life's diversity. Yet understanding the evolution of species radiations and how genome evolution progresses in this context remains a central problem in biology. Members of the rose family (Rosaceae) include familiar domesticates such as roses, apples, peaches, almonds, strawberries, and cherries. An intriguing and important radiation within Rosaceae produced the apple, pear, and quince genera, along with several valuable ornamentals. These are members of a clade of about 750 woody species distributed in 35 genera with a base chromosome number of x = 17 (tribe Maleae). The sister group of this clade is the genus Gillenia, which has just two species, both herbaceous perennials with a base chromosome number of x = 9. The Maleae are particularly attractive for the study of genome evolution in the context of a species radiation because of their generally small genome sizes and monophyletic roots in a single whole genome duplication (WGD) that postdates their divergence from Gillenia. Early diverging Maleae are similar to Gillenia in having dry fruits and few species. But after the evolution of the pome, the fleshy fruit found in most Maleae and the basis for their economic importance, they diversified into 32 genera, sorting into lineages with distinctive phenotypic, life history, and ecological traits, including lineages in which repeated hybridization and polyploidy events have contributed to their species-richness. This project will test the hypothesis that the infusion of a vast numbers of duplicate genes via WGD provided evolutionary potential for the radiating Maleae. The specific aims are to: (1) generate genome sequence from a small number of diploid genomes (both pre- and post-WGD) and determine the extent to which genic regions can be assembled and the history of duplicated genes reconstructed in selected Maleae genera; and, (2) establish the best sequencing and assembly approaches for the genome scan of a diploid/tetraploid species pair in Maleae. If successful, the project will provide resources for advancing our understanding of the evolution of economically and ecologically important processes such as fruit development, volatile production, changes in climate tolerance, and resistance to pests through the generation of thousands of new markers for breeding programs as well as genome sequences from two closely related species of Malus that differ with respect to ploidy. This project will provide research training for a postdoctoral fellow and a faculty member from Fitchburg State University, a primarily undergraduate institution in Massachusetts. All sequence data will be deposited and accessible through GenBank and the Genome Database for Rosaceae (GDR; www.rosaceae.org).

PI：莎拉·马修斯（Sarah Mathews）（哈佛大学）主要合作者：Erin Macneal Rehrig（Fitchburg State University）物种辐射是进化的引人注目的特征，可能是人生多样性的责任。然而，了解物种辐射的演变以及在这种情况下基因组进化如何发展仍然是生物学的核心问题。玫瑰家族的成员（酒渣鼻）包括熟悉的家人，例如玫瑰，苹果，桃子，杏仁，草莓和樱桃。酒渣鼻科内的有趣而重要的辐射产生了苹果，梨和木瓜属，以及几个有价值的装饰品。这些是大约750种木质物种的进化枝的成员，该物种分布在35属中，基本染色体数为X = 17（Maleae Tribe Maleae）。 The sister group of this clade is the genus Gillenia, which has just two species, both herbaceous perennials with a base chromosome number of x = 9. The Maleae are particularly attractive for the study of genome evolution in the context of a species radiation because of their generally small genome sizes and monophyletic roots in a single whole genome duplication (WGD) that postdates their divergence from Gillenia.早期分歧的乳腺癌与吉利尼亚的干果和少量物种相似。但是，在大多数肉食中发现的肉质果实以及其经济重要性的基础之后，它们分为32属，分为具有独特的表型，生命史和生态特征的谱系，包括重复的杂交和多倍杂交事件，有助于其物种富集。 该项目将检验以下假设：通过WGD输注大量重复基因为辐射性乳腺癌提供了进化潜力。具体目的是：（1）从少数二倍体基因组（WGD前后）产生基因组序列，并确定可以组装基因区域的程度，并在选定的Maleae属中重建的重复基因的历史； （2）为Maleae中二倍体/四倍体物种对的基因组扫描建立最佳的测序和组装方法。 如果成功，该项目将提供资源，以促进我们对经济和生态重要过程的发展，例如水果发展，挥发性的生产，气候耐受性的变化以及对虫害的抵抗，通过成千上万的新标记来育种计划以及来自两个与蛋白质相差的近距离相关物种的基因组序列以及基因组序列。 该项目将为博士后研究员和菲奇堡州立大学的一名教职员工提供研究培训，该大学主要是马萨诸塞州的本科机构。 所有序列数据将通过GenBank和可访问性的基因组数据库（GDR; www.rosaceae.org）沉积和访问。