プラナリアゲノムプロジエクト：ゲノム情報を用いた再生遺伝子ネットワーク解析

扁虫是一种非寄生扁形蠕虫，以其再生能力和在进化过程中获得了非常早期的功能大脑结构而闻名。日本涡虫是一种广泛分布于远东地区的典型浮游动物物种。细胞和分子实验方法已被广泛发展，以确定该物种中数千个基因的功能，这使这种浮游动物成为一个很好的实验模型。然而，目前还没有关于这种动物的基因组信息，而且到目前为止还没有发现多少基因调控机制。为了获得该物种的整体遗传信息并研究其基因调控机制，我们首先从实验室培育的无性克隆株中提取基因组DNA，并对476 GB的数据进行了第二代测序。Kmer频率分布图和FOSMID序列分析表明，这是一个复杂的基因组，使用双端测序数据很难组装。因此，我们采用了一种新的组装策略，并成功地改进了从头开始的基因组组装。获得了1.56 GB的基因组序列(包括213,090个骨架和23,204bp的N50长度)。为了寻找可能的基因调控机制，我们进一步分析了两个脊椎动物基因组之间的保守非编码元件(CNE)，并进行了转基因实验，证明Djndk基因中的CNE是一个调节元件。因此，这个基因组草案和基于它的CNE分析将对未来的脊椎动物研究有许多长期的好处。

Planarian is a non-parasitic Platyhelminthes (flatworm) that is famous for its regeneration ability and for having acquired a very early functional brain structure during evolution. Dugesia japonica is a typical planarian species widely spread in the Far East. Cellular and molecular experimental methods have been extensively developed to identify the functions of thousands of genes in this species, which have made this planarian a good experimental model. However, no genome information is available for this animal, and few gene regulatory mechanisms have been identified thus far. To obtain the overall genetic information of this species and to study its gene regulatory mechanisms, we firstly extracted genomic DNA from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. The Kmer frequency distribution graph and fosmid sequences analysis indicated a complicated genome that would be difficult to assemble by using pair-end sequencing data. Therefore, we used a new assembly strategy and successfully improved the de novo genome assembly. As a result, a 1.56 Gb genome sequence (including 213,090 scaffolds and N50 length 23,204bp) was achieved. To search for possible gene regulatory mechanisms, we further analyzed the conserved non-coding elements (CNEs) between two planarian genuses, and performed transgenic experiments that proved that a CNE in the Djndk gene is a regulatory element. Thus, this draft genome and CNE analysis based on it will have many long-term benefits for planarian research in the future.