De novo assembly and annotation of Didymium iridis transcriptome and identification of stage-specfic genes
Didymium iridis is a model organism whose cell types can be triggered by environmental stimuli or artificial intervention. However, the mechanism of regulation of cell type transformation is still little known. In this study, the genes transcribed during four different ontogenetic stages of D. iridis were analyzed by high throughput sequencing. A total of 37,792 Unigenes was assembled in which 24,523 unigenes and were identified the differentially expressed genes (DEGs) among different group samples by variation expression analysis. The DEGs were mainly involved in the Gene Ontology classification, like cellular processes, metabolic processes, receptor activity, and nucleic acid binding transcription factor activity, developmental process and growth. The DEGs from our samples were significantly enriched in metabolic pathways, such as starch and sucrose metabolism, RNA polymerase, the MAPK signaling pathway and fatty acid metabolism. Seven novel genes related to development and growth regulation were found, whose expression patterns were consistent with the results of trranscriptome sequencing. These results add to the available genetic data of D. iridis and and to the further understanding of the developmental processes in complex life cycles.
KeywordsSlime mold Didymium iridis Transcriptome Ontogenetic stages
(Clusters of Orthologous Groups)
(differentially expressed genes)
(false discovery rate)
(Kyoto Encyclopedia of Genes and Genomes)
(Reads per Kb per Million reads)
We thank the Beijing Genomics Institute at Shenzhen (BGI Shenzhen) for their assistance with sequencing, and also thank Meiping Zhang and Kangyu Wang analysis, or interpretation of data for the work.
Natural Science Foundation of China (NSFC) Grant 31770012.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
- Clark J, Stephenson SL, Landolt JC (2001) Biosystematics of the didymium iridis super species complex: additional isolates. Mycotaxon 79:447–454Google Scholar
- Feng C, Ming C, Xu CJ et al (2012) Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. BMC Genomics 13:1471–1486Google Scholar
- Jiang SC, Zhang B, Li YS, Li Y (2016) Optimization of axenic culture conditions of Myxomycete Didymium iridis. Mycosystema 35(5):641–644Google Scholar
- Kopp D (2012) Assembly of the Didymium Iridis mitochondrial genome by genome walking. Thesis. department of Biological Science, DePaul University, http://via.library.depaul.edu/csh_etd/20
- Pauline S, Israel B, Pat M et al (2015) The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Genome Biol Evol 8(1):109–125Google Scholar
- Rätzel V, Marwan W (2015) Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation. Dev Growth Differ 57:408-420. https://doi.org/10.1111/dgd.12220
- Schreckenbach T, Werenskiold A K (1986) Gene expression during plasmodial differentiation[M]. The Molecular Biology of Physarum polycephalum. Springer, New York, pp 131–150Google Scholar