Unraveling the evolutionary history of the green algae and their genomes

绿藻代表了最成功的光合作用真核生物之一，但令人惊讶的是，人们对它们的进化史知之甚少。大约在4.5亿-5亿年前，淡水绿藻的一个子集产生了第一批陆地植物。与陆地植物一起，绿藻构成了所谓的绿色谱系或病毒科。绿藻纲由两个部分组成：绿藻门和链藻门，前者包含大多数绿藻，后者包含所有陆地植物及其最接近的绿藻近亲，称为轮藻。*了解各种绿藻在生命树中的位置对于确定它们对不同环境的非凡适应背后的创新是至关重要的。为了破译主要绿藻谱系之间的系统发育关系，我的研究团队一直在分析在叶绿体和线粒体中发现的基因组。事实上，我们已经开创了这种比较基因组学方法来研究绿藻。我们已经证明，叶绿体(Cp)基因组是系统发育推断的有用数据来源，与陆地植物所观察到的相反，它在绿藻多样化过程中经历了巨大的变化。编码cp基因组标志的rRNA操纵子反向重复序列(IR)在绿藻中经历了多次扩张/收缩和大量丢失；然而，尽管IR具有重要的功能，但IR丢失的机制(S)仍不清楚。*这一建议解决了绿藻及其基因组进化的基本问题。为了实现所描述的4个目标中的3个，将研究来自3个不同进化节点的分类群的cp基因组。这些目的之一是为了更好地了解IR的作用和性质以及IR丢失的机制；拟议的分析是基于我们最近的发现，即2个IR拷贝在Ulvophyceae的3个谱系中顺序分化，并且这一史无前例的发现与我们为Ulotrichales提出的IR丢失的新模型相一致。在另一条创新的研究路线中，我们计划研究两个原生植物的核基因组结构，这些谱系被认为是所有核心叶绿体的姐妹(所谓的支系VII)；目标是深入了解这些藻类的生物学，以及在从原生植物向核心叶绿体转变过程中发生的基因组变化，大约900 mya。这些大规模的基因组研究也可能促进关于藻类适应高盐度的知识。*拟议的研究将为基因组学和生物信息学领域的研究生和本科生提供高质量的培训机会。由于这些科学领域有多个应用领域，该提案有望为加拿大的经济和社会健康做出贡献。

The green algae represent one of the most successful groups of photosynthetic eukaryotes, but surprisingly little is known about their evolutionary history. About 450-500 million years ago (mya), a subset of freshwater green algae gave rise to the first land plants. Together with the land plants, green algae constitute the so-called green lineage or Viridiplantae. The Viridiplantae comprises 2 divisions: the Chlorophyta, containing the majority of the green algae, and the Streptophyta, containing all land plants and their closest green algal relatives, known as charophytes.*** Knowledge about the positions of the diverse green algal groups in the tree of life is essential for identifying the innovations underlying their remarkable adaptations to different environments. To decipher the phylogenetic relationships among major green algal lineages, my research team has been analyzing the genomes found in the chloroplasts and mitochondria. As a matter of fact, we have pioneered this comparative genomic approach for the study of green algae. We have shown that the chloroplast (cp) genome is a useful source of data for phylogenetic inference and that, contrary to what has been observed for land plants, it underwent tremendous changes during green algal diversification. The rRNA operon-encoding inverted repeat (IR) – a hallmark of the cp genome – experienced multiple waves of expansion/contraction and numerous losses in green algae; however, despite the suggested functional importance of the IR, the mechanism(s) underlying IR loss remain unclear.*** This proposal addresses fundamental issues on the evolution of chlorophytes and their genomes. To achieve 3 of the 4 delineated objectives, cp genomes of taxa from 3 distinct evolutionary nodes will be investigated. One of these objectives is to better understand the roles and properties of the IR along with the mechanisms of IR loss; the proposed analyses are based on our recent findings that the 2 IR copies diverged in sequence in 3 lineages of the Ulvophyceae and that this unprecedented discovery is compatible with a novel model of IR loss we proposed for the Ulotrichales. In another innovative line of inquiry, we plan to study the nuclear genome architectures of 2 prasinophytes from the lineage presumed to be sister to all core chlorophytes (the so-called clade VII); the goals are to gain insights into the biology of these algae and into the genomic changes that occurred during the transition from prasinophytes to core chlorophytes about 900 mya. These large-scale genomic studies are also likely to advance knowledge about algal adaptation to high salinity.*** The proposed research will provide high-quality training opportunities for graduate and undergraduate students in the areas of genomics and bioinformatics. Because these fields of science have multiple application domains, the proposal is expected to contribute to the economic and societal health of Canada.