Microbial Genome Sequencing: Stramenopile Genomics: Comparative Chloroplast Sequencing

光合层藻是一类藻类，其存在对全球生态系统的功能是不可或缺的。这个多样化的分类群由数千个物种组成，包括单细胞和巨大的复杂的多细胞生物，代表了一个进化上不同的自养生物谱系，与红藻和绿藻系分开。叶绿体基因组已成为解读陆生植物谱系之间进化关系的首选工具，因为它们提供了一种直接和低成本的方法，可以从大量的分类群中获得大量的直向同源基因座（与核基因组测序相比）。因此，我们对叶绿体遗传结构和质体-宿主基因转移事件的了解大多来自对陆生植物的分析。到目前为止，只有两个叶绿体基因组已公布的整个stragalicile谱系。 这个数据集的最小尺寸是令人惊讶的，考虑到种子的作用，strageliles提供了各种水生群落和它们独特的分类地位。本研究的目的是对10个草莓属植物的叶绿体基因组DNA进行测序。目标生物体代表公认的16类层状菌中的9类。除了它们的分类多样性之外，这些藻类在形态上差异很大（包括单细胞、群体和大型藻类形式），并具有重大的生态或经济影响。 通过比较基因组测序分析层形藻叶绿体将：（a）深入了解这一相对未被探索的自养谱系中的叶绿体进化过程;（B）产生用于其他层形藻系统发育分析的序列数据库;（c）使得能够设计新的引物来探索浮游植物天然种群的多样性或基因表达;（d）提供用于比较叶绿体转录程序的遗传工具（例如，当细胞暴露于特定的环境挑战时）;（e）允许使用生物化学和生物信息学技术对结构/功能关系进行比较分析。 一个专门介绍藻类叶绿体基因组学的网站将传播该项目产生的数据，并将作为一个宣传工具，对公众进行关于这一全球重要藻类群体的教育。

Photosynthetic stramenopiles encompass a group of algae whose existence is indispensable to global ecosystem function. This diverse taxon consists of thousands of species, including both unicells and massive, complex multicellular organisms, representing an evolutionarily distinct lineage of autotrophs, separate from both the rhodophytic and chlorophytic lines. Chloroplast genomes have become a tool of choice in deciphering evolutionary relationships among terrestrial plant lineages, because they offer a straightforward and low cost means of obtaining numerous orthologous loci from a large number of taxa (compared to nuclear genome sequencing). For this reason, much of our knowledge concerning chloroplast genetic architecture and plastid-host gene transfer events is derived from the analysis of terrestrial plants. To date, only two chloroplast genomes have been published from the entire stramenopile lineage. The minimal size of this data set is surprising considering the seminal role stramenopiles provide in a variety of aquatic communities and their distinct taxonomic position. The goal of this research: to sequence chloroplast genomic DNA of ten stramenopiles. The targeted organisms represent nine of the recognized sixteen classes of stramenopiles. In addition to their taxonomic diversity, these algae differ extensively in morphology (encompassing unicells, colonial and macro algal forms) and have significant ecological or economic impact. Analysis of stramenopile chloroplasts via comparative genome sequencing will: (a) give insight into chloroplast evolutionary processes in this relatively unexplored autotrophic lineage; (b) generate a sequence database for use in the phylogenetic analysis of other stramenopiles; (c) enable the design of new primers to explore diversity or gene expression in natural populations of phytoplankton; (d) provide genetic tools for comparing chloroplast transcriptional programs (e.g., as cells are exposed to specific environmental challenges); (e) allow comparative analysis of structure/function relationships using biochemical and bioinformatic techniques. A web site dedicated to stramenopile chloroplast genomics will disseminate the data generated by the project and will also serve as an outreach vehicle for public education about this globally important group of algae.