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Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midguts of eastern honeybee workers

  • Dafu Chen
  • Huazhi Chen
  • Yu Du
  • Zhiwei Zhu
  • Jie Wang
  • Sihai Geng
  • Cuiling Xiong
  • Yanzhen Zheng
  • Chunsheng Hou
  • Qingyun Diao
  • Rui GuoEmail author
Genomics, transcriptomics, proteomics

Abstract

Currently, knowledge of circular RNAs (circRNAs) in insects including honeybee is extremely limited. Here, differential expression profiles and regulatory networks of circRNAs in the midguts of Apis cerana cerana workers were comprehensively investigated using transcriptome sequencing and bioinformatics. In total, 9589 circRNAs (201–800 nt in length) were identified from 8-day-old and 11-day-old workers’ midguts (Ac1 and Ac2); among them, 5916 (61.70%) A. cerana cerana circRNAs showed conservation with our previously indentified circRNAs in Apis mellifera ligucstica workers’ midguts (Xiong et al., Acta Entomologica Sinica 61:1363–1375, 2018). Five circRNAs were confirmed by RT-PCR and Sanger sequencing. Interestingly, novel_circ_003723, novel_circ_002714, novel_circ_002451, and novel_circ_001980 were highly expressed in both Ac1 and Ac2. In addition, the source genes of circRNAs were involved in 34 GO terms including organelle and cellular process and 141 pathways such as endocytosis and Wnt signaling pathway. Moreover, 55 DEcircRNAs including 34 upregulated and 21 downregulated circRNAs were identified in Ac2 compared with Ac1. circRNA-miRNA regulatory networks indicated that 1060 circRNAs can target 74 miRNAs; additionally, the DEcircRNA-miRNA-mRNA networks suggested that 13 downregulated circRNAs can bind to eight miRNAs and 29 miRNA-targeted mRNAs, while 16 upregulated circRNAs can link to 9 miRNAs and 29 miRNA-targeted mRNAs. These results indicated that DEcircRNAs as ceRNAs may play a comprehensive role in the growth, development, and metabolism of the worker’s midgut via regulating source genes and interacting with miRNAs. Notably, eight DEcircRNAs targeting miR-6001-y were likely to be key participants in the midgut development. Our findings not only offer a valuable resource for further studies on A. cerana cerana circRNA and novel insights into understanding the molecular mechanisms underlying the midgut development of eastern honeybee but also provide putative circRNA candidates for functional research in the near future and novel biomarkers for identification of eastern honeybee species including A. cerana cerana and honeybee diseases such as chalkbrood and microsporidiosis.

Keywords

Apis cerana cerana Honeybee Midgut Circular RNA Competitive endogenous RNA Regulatory network Metabolism Immunity 

Notes

Acknowledgments

We thank the editor and the anonymous reviewers for their valuable comments which helped us to improve our manuscript. We also thank Xiaoxue Fan (College of Animal Sciences (College of Bee Sciences), Fujian Agriculture and Forestry University, China) and Yuanchan Fan (College of Animal Sciences (College of Bee Science, Fujian), Agriculture and Forestry University, China) for their constructive contribution to the discussion during the revision process.

Authors’ contribution

RG designed this study. DFC, HZC, YD, SHG, CLX, YZZ, and CSH carried out laboratory work. RG, DFC, QYD, and HZC performed bioinformatic analyses. RG, DFC, and HZC supervised the work and contributed to preparation of the manuscript. All authors read and approved the final manuscript.

Funding information

This work was founded by the National Natural Science Foundation of China (31702190) to RG, the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-44-KXJ7) to DFC, the Science and Technology Planning Project of Fujian Province (2018J05042) to RG, the Education and Scientific Research Program Fujian Ministry of Education for Young Teachers (JAT170158) to RG, the Outstanding Scientific Research Manpower Fund of Fujian Agriculture and Forestry University (xjq201814) to RG, and the Science and Technology Innovation Fund of Fujian Agriculture and Forestry University (CXZX2017342, CXZX2017343) to RG and DFC.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Supplementary material

253_2019_10159_MOESM1_ESM.pdf (259 kb)
ESM 1 (PDF 974 kb)
253_2019_10159_MOESM2_ESM.xlsx (974 kb)
ESM 2 (XLSX 258 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Dafu Chen
    • 1
  • Huazhi Chen
    • 1
  • Yu Du
    • 1
  • Zhiwei Zhu
    • 1
  • Jie Wang
    • 1
  • Sihai Geng
    • 1
  • Cuiling Xiong
    • 1
  • Yanzhen Zheng
    • 1
  • Chunsheng Hou
    • 2
  • Qingyun Diao
    • 2
  • Rui Guo
    • 1
    Email author
  1. 1.College of Animal Sciences (College of Bee Science)Fujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Institute of Apicultural ResearchChinese Academy of Agricultural SciencesBeijingChina

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