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Transcriptome analysis of scyphozoan jellyfish Rhopilema esculentum from polyp to medusa identifies potential genes regulating strobilation

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Abstract

Strobilation is a unique asexual reproduction mode of scyphozoan jellyfish, through which benthic polyp develops into pelagic medusa. It is an orderly metamorphosis process triggered by environmental signals. However, the knowledges of molecular mechanisms under the drastic morphological and physiological changes are still limited. In this study, the transcriptomes from polyps to juvenile medusae at different stages were characterized by RNA-seq in scyphozoan jellyfish Rhopilema esculentum. Among 96,076 de novo assembled unigenes, 7090 differentially expressed genes (DEGs) were identified during the developmental stages. The co-expression pattern analysis of DEGs yielded 15 clusters with different expression patterns. Among them, a cluster with 388 unigenes was related to strobila. In this specific cluster, the GO terms related to “sequence-specific DNA binding transcription factor activity” and “sequence-specific DNA binding” were significantly enriched. Transcription factors, including segmentation protein even-skipped-like, segmentation polarity protein engrailed-like, homeobox proteins Otx-like, Twist-like and Cnox2-Pc-like, as well as genes such as RxR-like and Dmrtf-like, were identified to be potentially involved in strobilation. Their expression patterns and the other 11 TFs/genes involved in strobilation were confirmed with qRT-PCR methods. The present study pointed out the role of transcription factors in strobilation and produced a list of novel candidate genes for further studies. It could provide valuable information for understanding the molecular mechanisms of jellyfish strobilation.

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Acknowledgments

We thank BMK Biotechnology Co., Ltd. for help with the Illumina sequencing of the cDNA library and bio-informatic analysis.

Funding

This study received grant from the National Natural Science Foundation of China (31702327) and Key Program for International S&T Cooperation Projects of China (2017YFE0111100-5).

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Authors and Affiliations

  1. Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

    Jianlong Ge, Changlin Liu, Jie Tan, Li Bian & Siqing Chen

  2. Laboratory for Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China

    Jianlong Ge, Changlin Liu, Jie Tan, Li Bian & Siqing Chen

Authors
  1. Jianlong Ge
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  2. Changlin Liu
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  3. Jie Tan
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  4. Li Bian
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  5. Siqing Chen
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Correspondence to Siqing Chen.

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Additional information

Communicated by Mark Q. Martindale

Electronic supplementary material

Supplementary Fig. 1

The saturation curve of transcriptome sequencing data in the 6 libraries. The x-axis is the number of reads (in units of 10^6) and the y-axis is the number of genes detected (in units of 10^3). (DOCX 211 kb)

Supplementary Fig. 2

The 20 most enriched GO terms in the strobila specific cluster. The number on the top of each bar indicates the gene number in each GO terms. (DOCX 85 kb)

Supplementary Fig. 3

Classification of differentially expressed TFs according to their family group. (DOCX 17 kb)

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Ge, J., Liu, C., Tan, J. et al. Transcriptome analysis of scyphozoan jellyfish Rhopilema esculentum from polyp to medusa identifies potential genes regulating strobilation. Dev Genes Evol 228, 243–254 (2018). https://doi.org/10.1007/s00427-018-0621-z

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  • DOI: https://doi.org/10.1007/s00427-018-0621-z

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