Comparative Genomics of a Species Radiation: Sequencing the Apple Tribe

Pi：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进化在这一背景下是如何进展的，仍然是生物学的一个中心问题。玫瑰家族(蔷薇科)的成员包括熟悉的驯养植物，如玫瑰、苹果、桃子、杏仁、草莓和樱桃。一种有趣而重要的辐射在蔷薇科内产生了苹果、梨和木瓜属，以及几种有价值的观赏植物。它们是一个分支的成员，约有750种木本植物，分布于35个属，染色体基数x=17(马来族)。这一分支的姐妹群是三七属，它只有两个种，都是多年生草本植物，基本染色体数为x=9。马来亚科植物特别适合在物种辐射的背景下研究基因组进化，因为它们的基因组大小通常很小，而且在单个全基因组复制(WGD)中的单系根发生在它们与三七属的分歧之后。早期分叉的马来亚科与吉列亚属相似，果实干燥，种类较少。但在梨果的进化之后，梨果是在大多数马来亚科中发现的肉质果实，也是其经济重要性的基础，它们分化为32个属，划分出具有独特表型、生活史和生态特征的谱系，包括反复杂交和多倍体事件导致其物种丰富的谱系。这个项目将检验这样一个假设，即通过WGD注入大量重复基因为辐射的马来提供了进化潜力。其具体目标是：(1)从少数二倍体基因组(WGD前和WGD后)生成基因组序列，并确定在选定的马来科属中基因区域可以组装的程度和重复基因重建的历史；以及(2)为马来科二倍体/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，通过产生数千个用于育种计划的新标记以及来自两个在倍性方面不同的密切相关苹果物种的基因组序列，来促进我们对重要的经济和生态过程的理解，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。该项目将为费奇堡州立大学的一名博士后研究员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是本科生的机构。所有序列数据将保存在GenBank和蔷薇科基因组数据库(GDR；www.rosaceae.org)上，并可通过它们进行访问。

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).