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著特征，可能是造成生命多样性的主要原因。然而，了解物种辐射的进化以及基因组在这种背景下如何进化仍然是生物学的核心问题。玫瑰科（蔷薇科）的成员包括熟悉的驯化品种，如玫瑰、苹果、桃子、杏仁、草莓和樱桃。蔷薇科中一个有趣而重要的分支产生了苹果属、梨属和榅桲属，以及一些有价值的观赏植物。这些是分布在35属的750个木本物种的分支的成员，基本染色体数为x = 17（马来族）。这个分支的姐妹群是吉勒尼亚属，它只有两个物种，都是多年生草本植物，基本染色体数为x = 9。马来科在物种辐射的背景下对基因组进化的研究特别有吸引力，因为它们通常较小的基因组大小和单一全基因组复制（WGD）的单系根，这是它们与吉莱尼亚科分化后的结果。早期分化的马来科在有干果和少种方面与马来科相似。但是，在梨果（在大多数马来科中发现的肉质果实）的进化及其经济重要性的基础之后，它们分化为32个属，分类为具有独特表型，生活史和生态特征的谱系，包括重复杂交和多倍体事件的谱系，这些谱系有助于其物种丰富度。该项目将验证通过WGD注入大量重复基因为辐射雄性提供进化潜力的假设。具体目的是：(1)从少数二倍体基因组（包括wgd前和wgd后）中生成基因组序列，并确定在选定的雄性属中可以组装的基因区域的程度和复制基因的历史；(2)建立马来科二倍体/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，该项目将提供资源，促进我们对经济和生态重要过程的进化的理解，如果实发育、挥发性生产、气候耐受性的变化和对害虫的抗性，通过为育种计划产生数千个新的标记，以及两种密切相关的、在倍性方面不同的苹果物种的基因组序列。该项目将为菲奇堡州立大学的一名博士后和一名教员提供研究培训，该大学是马萨诸塞州的一所主要的本科院校。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。