The C-Fern (Ceratopteris richardit) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly
The C-Fern (Ceratopteris richardit) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly
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DOI：
10.1038/s41598-019-53968-8
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发表时间：
2019-12-03
影响因子：
4.6
通讯作者：
Soltis, Douglas E.
中科院分区：
文献类型：
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作者：
Marchant, D. Blaine;Sessa, Emily B.;Soltis, Douglas E.
蕨类植物因拥有庞大的基因组和众多的染色体而臭名昭著。尽管有几十年的推测，蕨类植物的扩展基因组背后的过程尚不清楚，主要是由于缺乏一个测序的同孢蕨类基因组。缺乏这一关键资源不仅阻碍了对同源孢子蕨类植物不寻常的基因组特征的进化过程的调查，而且还阻碍了陆地植物基因组进化的合成。在这里，我们使用模式蕨类物种Ceratopteris richardii来解决这些过程（例如，多倍性，重复元件的扩散），通过这种方式，同孢蕨类植物典型的大基因组和高染色体数目可能已经进化并得以保持。我们直接比较了跨越绿色植物生命树的物种中的重复序列组成和基因组大小的多样性，以及水蕨属基于短和长的组装。我们发现的证据与一个单一的古老的多倍体事件在水蕨的进化历史的基础上的基因组和细胞遗传学数据，并在重复的比例类似于那些发现在大型开花植物基因组。这项研究提供了一个主要的垫脚石在陆地植物进化基因组学的理解，通过提供第一个同孢蕨类参考基因组，以及深入了解这些巨大的基因组的形成过程。
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and longread- based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.