, Volume 73, Issue 4, pp 393–402 | Cite as

De novo assembly and annotation of Didymium iridis transcriptome and identification of stage-specfic genes

  • Shicui Jiang
  • Bo Zhang
  • Yanshuang Li
  • Yu LiEmail author
Original Paper


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.


Slime mold Didymium iridis Transcriptome Ontogenetic stages 



(Clusters of Orthologous Groups)


(differentially expressed genes)


(false discovery rate)


(Kyoto Encyclopedia of Genes and Genomes)


(Gene Ontology)




(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.

Supplementary material

11756_2018_37_MOESM1_ESM.docx (14 kb)
Table S1 (DOCX 14 kb)


  1. Aldrich HC, Carroll G (1971) Synaptonemal complexes and meiosis in Didymium iridis: a reinvestigation. Mycologia 63(2):308–316CrossRefGoogle Scholar
  2. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bailey J, Cook LJ, Kilmer-Barber R, Swanston E, Solnica-Krezel L, Lohman K, Dove WF, Dee J, Anderson RW (1999) Identification of three genes expressed primarily during development, in Physarum polycephalum. Arch Microbiol 172(6):364–376CrossRefPubMedGoogle Scholar
  4. Bernier F, Pallotta D, Lemieux G (1986a) Molecular cloning of mRNAs expressed specifically during spherulation of Physarum polycephalum. Biochim Biophys Acta 867(4):234CrossRefPubMedGoogle Scholar
  5. Bernier F, Seligy VL, Pallotta D, Lemieux G (1986b) Changes in gene expression during spherulation in Physarum polycephalu. Biochem Cell Biol 64(4):337–343CrossRefGoogle Scholar
  6. Clark J (1980a) Competition between Plasmodial-incompatibility phenotypes of the Myxomycete Didymium iridis. I. Paired plasmodia. Mycologia 72(2):312–321CrossRefGoogle Scholar
  7. Clark J (1980b) Competition between Plasmodial-incompatibility phenotypes of the Myxomycete Didymium iridis. II. Multiple-clone crosses. Mycologia 72(3):512–522CrossRefGoogle Scholar
  8. Clark J (1991) Didymium iridis mating systems: partial compatibility between mating series. Mycologia 83(2):210–213CrossRefGoogle Scholar
  9. Clark J, Lott T (1981) Aging in the acellular slime mold Didymium iridis: temperature and nutritional effects. Exp Mycol 5(4):369–372CrossRefGoogle Scholar
  10. Clark J, Stephenson SL, Landolt JC (2001) Biosystematics of the didymium iridis super species complex: additional isolates. Mycotaxon 79:447–454Google Scholar
  11. Clark J, Haskins EF, Stephenson SL (2004) Culture and reproductive systems of 11 species of Mycetozoans. Mycologia 96:36–40CrossRefPubMedGoogle Scholar
  12. Collins OR (1963) Multiple alleles at the incompatibility locus in the myxomycete Didymium iridis. Am J Bot 50(5):477–480CrossRefGoogle Scholar
  13. Collins OR (1976) Heterothallism and homothallism: a study of 27 isolates of Didymium iridis, a true slime mold. Am J Bot 63(2):138–143CrossRefGoogle Scholar
  14. Collins OR (1979) Myxomycete biosystematics: some recent developments and future research opportunities. Bot Rev 45(2):145–201CrossRefGoogle Scholar
  15. Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefPubMedGoogle Scholar
  16. 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
  17. Glöckner G, Golderer G, Werner Felmayer G (2008) A first glimpse at the transcriptome of Physarum polycephalum. BMC Genomics 9:1–11CrossRefGoogle Scholar
  18. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652CrossRefPubMedPubMedCentralGoogle Scholar
  19. Heidel AJ, Lawal HM, Felder M et al (2011) Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res 21:1882–1891CrossRefPubMedPubMedCentralGoogle Scholar
  20. Hendrickson PG, Silliker ME (2010a) RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis. Curr Genet 56(3):203–213CrossRefPubMedGoogle Scholar
  21. Hendrickson PG, Silliker ME (2010b) RNA editing is absent in a single mitochondrial gene of Didymium iridis. Mycologia 102(6):1288–1294CrossRefPubMedGoogle Scholar
  22. Jiang SC, Zhang B, Li YS, Li Y (2016) Optimization of axenic culture conditions of Myxomycete Didymium iridis. Mycosystema 35(5):641–644Google Scholar
  23. Johansen S, Vogt VM (1994) An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing. Cell 76:725–734CrossRefPubMedGoogle Scholar
  24. Johansen S, Elde M, Vader A, Haugen P, Haugli K, Haugli F (1997) In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis. Mol Microbiol 24:737–745CrossRefPubMedGoogle Scholar
  25. Keller HW, Schoknecht JD (1989) Life cycle of a new annulate spored species of Didymium. Mycologia 81(2):248–265CrossRefGoogle Scholar
  26. Kopp D (2012) Assembly of the Didymium Iridis mitochondrial genome by genome walking. Thesis. department of Biological Science, DePaul University,
  27. Kroneder R, Cashmore AR, Marwan W (1999) Phytochrome-induced expression of lig1, a homologue of the fission yeast cell-cycle checkpoint gene hus1, is associated with the developmental switch in Physarum polycephalum plasmodia. Curr Genet 36(1-2):86–93CrossRefPubMedGoogle Scholar
  28. Martel R, Tessier A, Pallotta D, Lemieux G (1988) Selective gene expression during sporulation of Physarum polycephalum. J Bacteriol 170(10):4784CrossRefPubMedPubMedCentralGoogle Scholar
  29. Marwan W (2003) Theory of time-resolved somatic complementation and its use to explore the sporulation control network in Physarum polycephalum. Genetics 164(1):105PubMedPubMedCentralGoogle Scholar
  30. Marwan W, Sujatha A, Starostzik C (2005) Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation. J Theor Biol 236(4):349–365CrossRefPubMedGoogle Scholar
  31. Materna SC, Marwan W (2005) Estimating the number of plasmids taken up by a eukaryotic cell during transfection and evidence that antisense RNA abolishes gene expression in Physarum polycephalum. Fems Microbiol Lett 243(1):29–35CrossRefPubMedGoogle Scholar
  32. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264CrossRefPubMedGoogle Scholar
  33. Mortazavi A, Williams B, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–626CrossRefPubMedGoogle Scholar
  34. Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M (2008) KEGG atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36:W423–W426CrossRefPubMedPubMedCentralGoogle Scholar
  35. 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
  36. Rätzel V, Ebeling B, Hoffmann XK, Tesmer J, Marwan W (2013) Physarum polycephalum mutants in the photocontrol of sporulation display altered patterns in the correlated expression of developmentally regulated genes. Develop Growth Differ 55(2):247–259CrossRefGoogle Scholar
  37. 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.
  38. Rojas C, Zúñiga JM, Stephenson SL (2015) Ecological niche modeling of some Costa Rican myxomycetes. Curr Res Environ Appl Mycol 5:153–159CrossRefGoogle Scholar
  39. Scheer MA, Silliker ME (2006) Mitochondrial inheritance patterns in Didymium iridis are not influenced by stage of mating competency. Mycologia 98(1):51–56CrossRefPubMedGoogle Scholar
  40. 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
  41. Sucgang R, Kuo A, Tian X et al (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 12:R20 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Sujatha A, Balaji S, Devi R, Marwanb W (2005) Isolation of Physarum polycephalum, plasmodial mutants altered in sporulation by chemical mutagenesis of flagellates. Eur J Protistol 41(1):19–27CrossRefGoogle Scholar
  43. Sweeney GE, Watts DI, Tumock G (1987) Differential gene expression during the amoebal-plasmodial transition in Physarum. Nucleic Acids Res 15(3):933–945CrossRefPubMedPubMedCentralGoogle Scholar
  44. Tang Y, Nielsen H, Masquida B, Gardner PP, Johansen SD (2014) Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Mob DNA 5:25. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Traphagen SJ (2010) RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum. RNA 16(4):828–838CrossRefPubMedPubMedCentralGoogle Scholar
  46. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63CrossRefPubMedPubMedCentralGoogle Scholar
  47. Watkins RF, Gray MW (2008) Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp. Protist 159:269–281CrossRefPubMedGoogle Scholar
  48. Wilke A, Harrison T, Wilkening J et al (2012) The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC bioinformatics 13:141. CrossRefPubMedPubMedCentralGoogle Scholar
  49. Ye J, Fang L, Zheng H et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297CrossRefPubMedPubMedCentralGoogle Scholar
  50. Yip V, Beekman M, Latty T (2014) Foraging strategies of the acellular slime moulds Didymium iridis and Didymium bahiense. Fungal Ecol 11:29–36CrossRefGoogle Scholar

Copyright information

© Institute of Molecular Biology, Slovak Academy of Sciences 2018

Authors and Affiliations

  1. 1.Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal FungiJilin Agricultural UniversityChangchun CityPeople’s Republic of China
  2. 2.Agricultural college, MOE Key Laboratory of Natural Resources of the Changbai Mountain and Functional MoleculesYanbian UniversityYanji CityPeople’s Republic of China

Personalised recommendations