Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far. To obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates. This draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp .

中文翻译：

---

Dugesia japonica 基因组草图提供了对涡虫大脑限制基因 nou-darake 的保守调控元件的见解

涡虫是非寄生扁形虫（扁虫），以其再生能力和组织良好的大脑而闻名。Dugesia japonica是一种典型的涡虫物种，广泛分布于东亚地区。已经开发了广泛的细胞和分子实验方法来识别该物种中数千个基因的功能，使这种涡虫成为再生生物学和神经生物学的良好实验模型。然而，没有可用于 D. japonica 的基因组水平信息，并且迄今为止已经确定了很少的基因调控网络。为了获得该物种的全基因组信息并研究其基因调控网络，我们从实验室培育的无性克隆菌株衍生的 200 只涡虫中提取了基因组 DNA，并通过第二代测序对 476 Gb 的数据进行了测序。Kmer 频率图和 fosmid 序列分析表明，使用第二代测序短读长难以组装的复杂基因组。为了应对这一挑战，我们开发了一种新的组装策略并改进了从头基因组组装，产生了一个 1.56 Gb 基因组序列（DjGenome ver1.0，包括 202,925 个支架和 N50 长度 27,741 bp），涵盖了基因组中所有 19,543 个基因的 99.4%。组装的转录组，尽管基因组是碎片化的，因为 80% 的基因组由重复序列组成（基因组频率≥ 2）。通过两个涡虫属之间的基因组比较，我们确定了保守的非编码元件 (CNE)，它们指示基因调控元件。使用非洲爪蟾的转基因实验表明 Djndk 基因中的一个 CNE 可能是一个调节元件，提示ndk基因的调控和脑形成机制在脊椎动物和无脊椎动物之间可能是保守的。该基因组草图和 CNE 分析将有助于解决涡虫的基因调控网络。基因组数据库可在以下网址获得：http://www.planarian.jp。