Impact of secondary endosymbiosis on eukaryotic genome evolution

内共生过程在真核生物（含核）的起源和多样化中起着巨大的作用。质体（叶绿体）最初的内共生起源发生在10亿多年前，并产生了三个分支——绿藻（及其陆生植物亲戚）、红藻和蓝藻——它们的能量生成能力为生物圈的转变铺平了道路。红藻和绿藻的光合作用细胞器通过“次生内共生”扩散到不相关的真核生物中——藻类细胞被吞噬并保留在非光合作用宿主体内。次生内共生已经产生了地球上一些最丰富和生态意义最大的水生光合作用者，包括异藻（如硅藻和巨藻）和引起“赤潮”的鞭毛藻。我们正在领导一个由美国能源部联合基因组研究所（JGI）资助的项目，对两种具有关键进化和细胞生物学意义的含二次质体藻类——隐单胞菌吉拉迪亚和绿蛛纲植物Bigelowiella natans——的核基因组进行测序。总之，这些生物的独特之处在于它们仍然以高度还原和简化的形式拥有其藻内共生体的核（核形态）和细胞质。隐单胞虫和绿蛛形虫核形的有限编码能力表明，这些生物的核基因组在其进化史上已经成为数千个内共生源基因的储存库。该项目的目标是：(1)带领社区努力“注释”吉迪亚和Bigelowiella基因组序列；(2)建立生物信息学资源，用于存储、管理和分析我们的全基因组数据集；(3)执行与DOE-JGI项目主要目标相关的各种基因组分析。比较和对比吉迪亚菌和比格洛韦氏菌的基因组序列，将为从遗传、生化和细胞水平上了解次生内共生过程以及各自宿主和内共生体的整合提供一个前所未有的窗口。

The process of endosymbiosis has been a monumental force in the origin and diversification of eukaryotic (nucleus-containing) organisms. The primary endosymbiotic origin of plastids (chloroplasts) occurred more than a billion years ago and spawned three lineages-the green algae (and their land plant relatives), red algae and glaucophytes-whose energy-generating capabilities paved the way for a transformation of the biosphere. The photosynthetic organelles of red and green algae have spread to unrelated eukaryotes by 'secondary endosymbiosis'-the engulfment and retention of an algal cell inside a non-photosynthetic host. Secondary endosymbiosis has given rise to some of the most abundant and ecologically significant aquatic photosynthesizers on the planet, including heterokonts (e.g., diatoms and giant kelp) and the 'red tide'-causing dinoflagellates. We are leading a DOE Joint Genome Institute (JGI)-funded effort to sequence the nuclear genomes of two secondary plastid-containing algae of pivotal evolutionary and cell biological significance, the cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. Together, these organisms are unique in that they still possess the nucleus (nucleomorph) and cytoplasm of their algal endosymbionts in a highly reduced and simplified form. The limited coding capacity of the cryptomonad and chlorarachniophyte nucleomorphs indicates that the nuclear genomes of these organisms have been repositories for thousands of endosymbiont-derived genes throughout their evolutionary history. The goal of this project is to (i) spearhead community efforts to 'annotate' the Guillardia and Bigelowiella genome sequences (ii) establish the bioinformatic resources with which to store, manage and analyze our whole genome datasets, and (iii) perform a variety of genomic analyses related to the DOE-JGI project's main goals. Comparing and contrasting the Guillardia and Bigelowiella genome sequences will provide an unprecedented window into the process of secondary endosymbiosis and the integration of their respective hosts and endosymbionts at the genetic, biochemical and cellular level.