| Regeneration has been a rather enigmatic topic in modern developmental biology. Partially, this is because the most spectacular regeneration occurs in organisms such as hydra or planarians that are not standard laboratory model organisms as yet. Therefore, the investigation of regeneration by using modern molecular genetics techniques has been limited, and regeneration is believed to utilize the same molecular mechanisms involved in embryonic Development. Planarians exhibit an extraordinary ability to regenerate lost body parts which is attributed to an abundance of pluripotent somatic stem cells called neoblasts; it is perfect organism model in regeneration and stem cell biology.In previous years, next-generation sequencing technology has emerged as a cutting-edge approach for high-throughput sequence determination, and this has dramatically improved the efficiency and speed of gene discovery. Illumina sequencing of transcriptomes for organisms with completed genomes confirmed that the relatively short reads thus produced can be effectively assembled and employed for gene discovery and comparison of gene expression profiles. Transcriptome-seq technology has been applied to human, yeast, mouse and Arabidopsis models, thus opening up the entire transcriptional landscape of gene activity and AS in a high-throughput and quantitative manner. Further, high-quality DNA sequence with Illumina technology demonstrated the suitability of short-read sequencing for de novo assembly and annotation of genes expressed in a eukaryote without prior genomic information. In addition, high-throughput sequencing technology also has a very wide range of applications in the Digital Gene Expression Profiles (DGE) system and the small RNA sequencing.In this article, we report a transcriptome sequence of a Planaria subspecies Dugesia japonica derived by high-throughput sequencing. Consequently,11,913,548transcriptome sequencing reads were obtained. Finally, these reads were eventually assembled into37,218unique unigenes. These assembled unigenes were annotated with various methods. As we know, this is the first time to report the planarian Dugesia japonica transcriptome.In addition, we researched transcriptome changes during different periods of regeneration by using a tag-based digital gene expression (DGE) system. Transcriptome changes during planarian regeneration were investigated by using a tag based DGE system. We choose three regenerative periods, Od, Id, and3d of regeneration, and we obtained a sequencing depth of more than3.5million tags per sample and identified a large number of differentially expressed tags at various stages of regeneration. After mapping these tags into reference genes, hundreds of change genes were detected. The results provide a fairly comprehensive molecular biology background to the research on planarian development, particularly with regard to its regeneration progress.Recently, small RNAs have been an increasing concern and studied in many aspects, including regeneration and stem cell biology, among others. In the current study, the large-scale cloning and sequencing of sRNAs from the intact and regenerative planarian Dugesia japonica are reported. Sequence analysis shows that sRNAs between18nt and40nt are mainly micro RNAs and piRNAs. In addition,209conserved miRNAs and12novel miRNAs are identified. Especially, a better screening target method, negative-correlation relationship of miRNAs and mRNA, is adopted to improve target prediction accuracy. Similar to miRNAs, a diverse population of piRNAs and changes in the two samples are also listed. The present study is the first to report on the important role of sRNAs during planarian regeneration. |
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