Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica

PLoS One. 2015 Nov 20;10(11):e0143525. doi: 10.1371/journal.pone.0143525. eCollection 2015.

Abstract

We established a laboratory clonal strain of freshwater planarian (Dugesia japonica) that was derived from a single individual and that continued to undergo autotomous asexual reproduction for more than 20 years, and we performed large-scale genome sequencing and transcriptome analysis on it. Despite the fact that a completely clonal strain of the planarian was used, an unusually large number of mutations were detected. To enable quantitative genetic analysis of such a unique organism, we developed a new model called the Reference Gene Model, and used it to conduct large-scale transcriptome analysis. The results revealed large numbers of mutations not only outside but also inside gene-coding regions. Non-synonymous SNPs were detected in 74% of the genes for which valid ORFs were predicted. Interestingly, the high-mutation genes, such as metabolism- and defense-related genes, were correlated with genes that were previously identified as diverse genes among different planarian species. Although a large number of amino acid substitutions were apparently accumulated during asexual reproduction over this long period of time, the planarian maintained normal body-shape, behaviors, and physiological functions. The results of the present study reveal a unique aspect of asexual reproduction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Animals
  • Cell Count
  • Clone Cells
  • Gene Expression
  • Gene Expression Profiling
  • Genome, Helminth*
  • Helminth Proteins / genetics*
  • Models, Genetic
  • Molecular Sequence Annotation
  • Mutation*
  • Open Reading Frames
  • Planarians / genetics*
  • Polymorphism, Single Nucleotide
  • Reproduction, Asexual / genetics*
  • Transcriptome*

Substances

  • Helminth Proteins

Grant support

This study was supported in part by the Frontier Research Program, a Grant-in-Aid for Global COE Program to KA (A06) (http://www.jsps.go.jp/j-globalcoe/05_kyoten.html), and a Grant-in-Aid for Creative Scientific Research to KA (17GS0318) (https://www.jsps.go.jp/j-grantsinaid/18_sousei/c_hyouka_kekka20.html) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.