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：Sarah Mathews（哈佛大学）主要合作者：Erin MacNeal Rehrig（菲奇堡州立大学）物种辐射是进化的一个显着特征，可能是生命多样性的重要原因。然而，了解物种辐射的进化以及基因组进化在这种情况下如何进展仍然是生物学的中心问题。玫瑰科（蔷薇科）的成员包括常见的驯化植物，如玫瑰、苹果、桃子、杏仁、草莓和樱桃。蔷薇科中一种有趣且重要的辐射产生了苹果、梨和木瓜属，以及一些有价值的观赏植物。这些是大约 750 个木本物种的分支成员，分布在 35 个属中，基本染色体数为 x = 17（马来族）。该分支的姐妹群是紫罗兰属，它只有两个物种，都是草本多年生植物，基本染色体数为 x = 9。马来亚科对于研究物种辐射背景下的基因组进化特别有吸引力，因为它们的基因组大小普遍较小，并且单系根源在于单个全基因组复制（WGD），该复制是在它们与紫罗兰属分歧之后出现的。早期分化的马来亚科与七彩亚科相似，有干果且种类较少。但在仁果（大多数马来亚种发现的肉质果实及其经济重要性的基础）的进化之后，它们多样化为 32 个属，分类为具有独特表型、生活史和生态特征的谱系，包括反复杂交和进化的谱系。多倍体事件促进了它们的物种丰富性。 该项目将检验这样一个假设：通过全基因组测序注入大量重复基因为辐射马来亚种提供了进化潜力。具体目标是：（1）从少量二倍体基因组（WGD前和WGD后）生成基因组序列，并确定基因区域可以组装的程度以及在选定马来亚属中重建重复基因的历史; (2) 建立马来亚二倍体/四倍体物种对基因组扫描的最佳测序和组装方法。 如果成功，该项目将通过为育种计划生成数千个新标记，为加深我们对经济和生态重要过程的演变的理解提供资源，例如水果发育、挥发性生产、气候耐受性的变化以及对害虫的抵抗力。以及两个密切相关的苹果属物种的基因组序列，它们在倍性方面有所不同。 该项目将为菲奇堡州立大学（马萨诸塞州的一所主要本科院校）的一名博士后研究员和一名教员提供研究培训。 所有序列数据将通过 GenBank 和蔷薇科基因组数据库（GDR；www.rosaceae.org）进行存储和访问。