Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida
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DOI：
10.1073/pnas.1221259110
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发表时间：
2013-03-26
影响因子：
11.1
通讯作者：
Boyen, Catherine
中科院分区：
文献类型：
--
作者：
Collen, Jonas;Porcel, Betina;Boyen, Catherine
红海藻是沿海生态系统的关键组成部分，作为食物和胶凝剂来源具有重要的经济意义，但它们的基因和基因组却很少受到关注。在这里，我们报告了花卉植物卷曲角叉菜（爱尔兰苔藓）105-Mbp 基因组的测序以及 9,606 个基因的注释。该基因组具有不寻常的结构，其特征是基因密集区域被转座元件主导的重复丰富区域包围。尽管其尺寸相当大，但该基因组显示出紧凑基因组的典型特征，例如。例如，每个基因平均只有 0.3 个内含子，内含子短，基因之间的中值距离低，基因家族小，并且没有大规模基因组重复的迹象。该基因组还深入了解海洋红藻的代谢和对海洋环境的适应，包括与卤素代谢、氧脂素和多细胞性（microRNA 处理和转录因子）相关的基因。特别有趣的是与碳水化合物代谢相关的特征，其中包括用于淀粉生物合成的简约基因集、在初级内共生之前获得的纤维素合酶的存在（显示古质体中纤维素合成的多系性）、陆地植物中不存在的纤维素酶以及可能源自海洋细菌的甘露糖基甘油酸合酶的出现。为了解释对基因组结构和基因内容的观察，我们提出了一种进化情景，涉及一种祖先红藻，它在早期生态力量的驱动下失去了基因、内含子和遗传间DNA；这种损失之后，由于转座元件的活性，基因组大小随之扩大。
Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e. g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.