EAGER: Collaborative Research: Plastid genome evolution in Cactaceae, a New World succulent radiation

该项目将研究开花植物仙人掌科仙人掌的基因组进化。仙人掌有1500种，是美洲干旱和半干旱地区最壮观、进化最成功的多肉植物群之一。尽管仙人掌科的生命形式非常多样，并且对干旱、炎热的栖息地具有极端的生理适应能力，但它们的基因组资源仍然非常有限。这个由亚利桑那州立大学、沙漠植物园和亚利桑那大学成员组成的研究小组将为我们了解仙人掌的物种多样性、生态学、光合作用和进化提供基本的基因组信息和资源，并在基础科学、园艺和经济领域产生预期的影响。来自科学领域代表性不足群体的本科生将在基因组学、生物信息学、计算、进化和系统生物学技术方面接受广泛的培训。该项目的成果将用于加强亚利桑那州立大学的本科遗传学课程和生物学教育网站，以及沙漠植物园的推广项目。该项目的所有数据将存入公共数据库。该项目将重点研究仙人掌中质体（即叶绿体）基因组的异常大小和重排，特别是在几个大型柱状北美物种中观察到的对光合作用过程至关重要的多个基因的丢失。生成的DNA序列数据将用于生成完整的质体基因组，以及从生态和形态多样化的仙人掌物种中识别多个核和线粒体基因。这将有助于研究特定结构基因组重排的分布和模式，并检验关于这些结构变化的原因和后果的假设。与此同时，该项目将提供数据，以产生一个更强大的系统发育框架，用于研究仙人掌科特定群体的进化关系，以及测量整个家族的分子进化和突变率。重建这个光合植物家族的基因丢失和基因组重组的历史，为研究沙漠环境中生命选择压力下的基因组变异和进化提供了一个系统。

This project will investigate genome evolution in cacti, the flowering plant family Cactaceae. The 1500 species of cacti are among the most spectacular and evolutionarily successful groups of succulent plants in arid and semi-arid regions of the Americas. Despite their remarkably diverse life forms and extreme physiological adaptations for life in arid, often hot habitats, genomic resources in Cactaceae are still very limited. This research team, with members from Arizona State University, the Desert Botanic Garden, and the University of Arizona, will provide fundamental genomic information and resources essential to our understanding of species diversity, ecology, photosynthesis and evolution of cacti, with expected impacts in basic science as well as horticultural and economic arenas. Undergraduates from underrepresented groups in science will be trained broadly in genomics, bioinformatics, computational, evolutionary and systematic biology techniques. Results from this project will be used to enhance an undergraduate genetics course and a biology education website at Arizona State University, and outreach programs at the Desert Botanical Garden. All data from the project will be deposited in public databases. This project will focus on the unusual size and rearrangements of the plastid (i.e., chloroplast) genome within cacti, and in particular the loss of multiple genes critical to the process of photosynthesis observed in several large columnar North American species. The DNA sequence data generated will be used to produce complete plastid genomes, as well as identify multiple nuclear and mitochondrial genes, from a broad sampling of ecologically and morphologically diverse cactus species. This will enable an investigation of the distribution and pattern of specific structural genomic rearrangements and test hypotheses about the causes and consequences of these architectural changes. At the same time, the project will contribute data to generate a more robust phylogenetic framework for investigating the evolutionary relationships of specific groups of Cactaceae, as well as measuring rates of molecular evolution and mutation across the family. Reconstructing the history of gene losses and genome reconfigurations in this family of photosynthetic plants offers a system for studying genome variation and evolution under the selective pressures of life in the desert environment.