@article {1538, title = {Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica}, journal = {PLoS ONE}, volume = {10}, year = {2015}, month = {2015}, pages = {e0143525}, publisher = {Public Library of Science}, address = {San Francisco, CA USA}, 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.

}, isbn = {1932-6203}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654569/}, author = {Nishimura, Osamu and Hosoda, Kazutaka and Kawaguchi, Eri and Yazawa, Shigenobu and Hayashi, Tetsutaro and Inoue, Takeshi and Umesono, Yoshihiko and Agata, Kiyokazu}, editor = {Fu, Binying} } @article {1493, title = {Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms}, journal = {PLoS ONE}, volume = {10}, year = {2015}, month = {2015}, pages = {e0120081}, publisher = {Public Library of Science}, address = {San Francisco, CA USA}, abstract = {

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

}, isbn = {1932-6203}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368550/}, author = {Sol{\`a}, Eduard and {\'A}lvarez-Presas, Marta and Fr{\'\i}as-L{\'o}pez, Cristina and Littlewood, D Timothy J and Rozas, Julio and Riutort, Marta}, editor = {Escriva, Hector} }