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Open Access Highly Accessed Research article

Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species

Osamu Nishimura12, Yukako Hirao23, Hiroshi Tarui24 and Kiyokazu Agata1*

Author Affiliations

1 Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan

2 Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Japan

3 Functional Probe Research Laboratory, RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Japan

4 LSA System Development Unit, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan

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BMC Genomics 2012, 13:289  doi:10.1186/1471-2164-13-289

Published: 29 June 2012



Planarians are considered to be among the extant animals close to one of the earliest groups of organisms that acquired a central nervous system (CNS) during evolution. Planarians have a bilobed brain with nine lateral branches from which a variety of external signals are projected into different portions of the main lobes. Various interneurons process different signals to regulate behavior and learning/memory. Furthermore, planarians have robust regenerative ability and are attracting attention as a new model organism for the study of regeneration. Here we conducted large-scale EST analysis of the head region of the planarian Dugesia japonica to construct a database of the head-region transcriptome, and then performed comparative analyses among related species.


A total of 54,752 high-quality EST reads were obtained from a head library of the planarian Dugesia japonica, and 13,167 unigene sequences were produced by de novo assembly. A new method devised here revealed that proteins related to metabolism and defense mechanisms have high flexibility of amino-acid substitutions within the planarian family. Eight-two CNS-development genes were found in the planarian (cf. C. elegans 3; chicken 129). Comparative analysis revealed that 91% of the planarian CNS-development genes could be mapped onto the schistosome genome, but one-third of these shared genes were not expressed in the schistosome.


We constructed a database that is a useful resource for comparative planarian transcriptome studies. Analysis comparing homologous genes between two planarian species showed that the potential of genes is important for accumulation of amino-acid substitutions. The presence of many CNS-development genes in our database supports the notion that the planarian has a fundamental brain with regard to evolution and development at not only the morphological/functional, but also the genomic, level. In addition, our results indicate that the planarian CNS-development genes already existed before the divergence of planarians and schistosomes from their common ancestor.