Comparative Genomics of a Species Radiation: Sequencing the Apple Tribe

主要研究者：萨拉马修斯（哈佛大学）主要合作者：艾琳麦克尼尔雷德里格（菲奇堡州立大学）物种辐射是进化的一个显著特征，可能是生命多样性的主要原因。然而，理解物种辐射的进化以及基因组进化如何在这种背景下进行仍然是生物学的中心问题。蔷薇科（蔷薇科）的成员包括熟悉的驯化植物，如玫瑰、苹果、桃、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、梨属和木瓜属，以及沿着几种有价值的植物。这些是分布在35个属中的约750个木本物种的分支的成员，基本染色体数目为x = 17（部落Maleae）。这个分支的姐妹群是Gillenia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。Maleae是特别有吸引力的基因组进化的研究中的一个物种的辐射，因为他们的基因组大小一般很小，单系根在一个单一的全基因组重复（WGD），postdates他们的分歧从Gillenia。早期分歧的Maleae类似于Gillenia，具有干果和少数种类。但是在梨果的进化之后，在大多数Maleae中发现的肉质果实及其经济重要性的基础，它们多样化为32个属，分为具有独特表型，生活史和生态特征的谱系，包括重复杂交和多倍性事件有助于其物种丰富度的谱系。 该项目将测试一个假设，即通过WGD注入大量的重复基因为辐射型马来族提供了进化潜力。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和在选定的马来族属中重建的重复基因的历史;以及（2）建立马来族中二倍体/四倍体物种对的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，以促进我们对经济和生态重要过程的进化的理解，如水果发育，挥发性生产，气候耐受性的变化，以及通过产生数千个新的育种计划标记以及来自两个密切相关的苹果属物种的基因组序列对倍性不同的害虫的抗性。 该项目将为马萨诸塞州的一所以本科为主的机构--菲奇堡州立大学的一名博士后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）保存和访问。

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).