02757nas a2200265 4500008004100000020001400041245017200055210006900227260005900296300001300355490000700368520186200375100001902237700001402256700001602270700001302286700001902299700001802318700001702336700002002353700001602373700001802389700002702407856005702434 2016 eng d a1932-620300aDe Novo Transcriptome Analysis Provides Insights into Immune Related Genes and the RIG-I-Like Receptor Signaling Pathway in the Freshwater Planarian (Dugesia japonica)0 aDe Novo Transcriptome Analysis Provides Insights into Immune Rel aSan Francisco, CA USAbPublic Library of Sciencec2016 ae01515970 v113 aBACKGROUND: The freshwater planarian Dugesia japonica (D. japonica) possesses extraordinary ability to regenerate lost organs or body parts. Interestingly, in the process of regeneration, there is little wound infection, suggesting that D. japonica has a formidable innate immune system. The importance of immune system prompted us to search for immune-related genes and RIG-I-like receptor signaling pathways. RESULTS: Transcriptome sequencing of D. japonica was performed on an IlluminaHiSeq2000 platform. A total of 27,180 transcripts were obtained by Trinity assembler. CEGMA analysis and mapping of all trimmed reads back to the assembly result showed that our transcriptome assembly covered most of the whole transcriptome. 23,888 out of 27,180 transcripts contained ORF (open reading fragment), and were highly similar to those in Schistosoma mansoni using BLASTX analysis. 8,079 transcripts (29.7%) and 8,668 (31.9%) were annotated by Blast2GO and KEGG respectively. A DYNLRB-like gene was cloned to verify its roles in the immune response. Finally, the expression patterns of 4 genes (RIG-I, TRAF3, TRAF6, P38) in the RIG-I-like receptor signaling pathway were detected, and the results showed they are very likely to be involved in planarian immune response. CONCLUSION: RNA-Seq analysis based on the next-generation sequencing technology was an efficient approach to discover critical genes and to understand their corresponding biological functions. Through GO and KEGG analysis, several critical and conserved signaling pathways and genes related to RIG-I-like receptor signaling pathway were identified. Four candidate genes were selected to identify their expression dynamics in the process of pathogen stimulation. These annotated transcripts of D. japonica provide a useful resource for subsequent investigation of other important pathways.1 aPang, Qiuxiang1 aGao, Lili1 aHu, Wenjing1 aAn, Yang1 aDeng, Hongkuan1 aZhang, Yichao1 aSun, Xiaowen1 aZhu, Guangzhong1 aLiu, Baohua1 aZhao, Bosheng1 aRobinson-Rechavi, Marc uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795655/02108nas a2200241 4500008004100000020001400041245010600055210006900161260005900230300001300289490000700302520131600309100002101625700002101646700001901667700002201686700002301708700001901731700002301750700002001773700001601793856005701809 2015 eng d a1932-620300aUnusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica0 aUnusually Large Number of Mutations in Asexually Reproducing Clo aSan Francisco, CA USAbPublic Library of Sciencec2015 ae01435250 v103 a

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.

1 aNishimura, Osamu1 aHosoda, Kazutaka1 aKawaguchi, Eri1 aYazawa, Shigenobu1 aHayashi, Tetsutaro1 aInoue, Takeshi1 aUmesono, Yoshihiko1 aAgata, Kiyokazu1 aFu, Binying uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654569/02292nas a2200217 4500008004100000020001400041245008200055210006900137260005900206300001300265490000700278520157600285100001801861700002701879700002801906700002701934700001701961700001901978700002001997856005702017 2015 eng d a1932-620300aEvolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms0 aEvolutionary Analysis of Mitogenomes from Parasitic and FreeLivi aSan Francisco, CA USAbPublic Library of Sciencec2015 ae01200810 v103 a

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.

1 aSolà, Eduard1 aÁlvarez-Presas, Marta1 aFrías-López, Cristina1 aLittlewood, Timothy, J1 aRozas, Julio1 aRiutort, Marta1 aEscriva, Hector uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368550/