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

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Abstract

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.

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Abbreviations

COG:

(Clusters of Orthologous Groups)

DEGs:

(differentially expressed genes)

FDR:

(false discovery rate)

KEGG:

(Kyoto Encyclopedia of Genes and Genomes)

GO:

(Gene Ontology)

NR:

(non-redundant)

RPKM:

(Reads per Kb per Million reads)

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Acknowledgments

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.

Funding

Natural Science Foundation of China (NSFC) Grant 31770012.

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Authors and Affiliations

  1. Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, People’s Republic of China

    Shicui Jiang, Bo Zhang, Yanshuang Li & Yu Li

  2. Agricultural college, MOE Key Laboratory of Natural Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Yanji City, People’s Republic of China

    Shicui Jiang

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  1. Shicui Jiang
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  2. Bo Zhang
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  4. Yu Li
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Correspondence to Yu Li.

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Jiang, S., Zhang, B., Li, Y. et al. De novo assembly and annotation of Didymium iridis transcriptome and identification of stage-specfic genes. Biologia 73, 393–402 (2018). https://doi.org/10.2478/s11756-018-0037-2

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