Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

• DOI: 10.1186/s40851-018-0102-2
• Publication Date: 2018-08-29T11:49:44Z
• Authors: Yang An; Akane Kawaguchi; Chen Zhao; Atsushi Toyoda; Ali Sharifi-Zarchi; Seyed Ahmad Mousavi; Reza Bagherzadeh; Takeshi Inoue; Hajime Ogino; Asao Fujiyama; Hamidreza Chitsaz; Hossein Baharvand; Kiyokazu Agata
• Keywords: 0301 basic medicine; Planarian; 03 medical and health sciences; Dugesia japonica; Genome; Nou-darake; Conserved Non-coding Elements ; Dugesia Japonica ; Genome ; Nou-darake ; Planarian; QL1-991; Conserved non-coding elements; Zoology; Research Article

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