Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection

Chen Huang, Dongliang Leng, Shixue Sun, Xiaohua Douglas Zhang

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Background: Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching. The fact that the breakdown of symbiosis between coral and the dinoflagellate, zooxanthellae, has been well elucidated as the main cause of bleaching, implying the establishment of symbiosis with zooxanthellae plays a crucial role in maintaining coral survival. However, the relevant molecular and cellular mechanisms have not been well studied yet. In this study, based on the deep RNA-sequencing data derived from Mohamed, A. R. et al., an integrated transcriptome analysis was performed to deeply investigate global transcriptome changes of the coral Acropora digitifera in response to infection by dinoflagellate of the genus Symbiodinium. Results: The results revealed that compared to RefTranscriptome-v1.0 (A. digitifera transcriptome assembly v1.0), numerous novel transcripts and isoforms were identified, the Symbiodinium-infected coral larvae at 4 h generated the highest proportion of specific isoforms. Alternative splicing analysis showed that intron retention predominated in all alternative transcripts among six statuses. Additionally, 8117 lncRNAs were predicted via a stringent stepwise filtering pipeline. A complex lncRNAs-mRNAs network including 815 lncRNAs and 6395 mRNAs were established, in which 21 lncRNAs were differentially expressed at 4 h post infection. Functional clustering analysis for those differentially lncRNAs-coexpressed mRNAs demonstrated that several biological processes and pathways related to protein kinase activity, metabolic pathways, mitochondrion, ribosome, etc. were enriched. Conclusions: Our study not only refined A. digitifera transcriptome via identification of novel transcripts and isoforms, but also predicted a high-confidence dataset of lncRNAs. Functional study based on the construction of lncRNAs-mRNAs co-expression network has disclosed a complex lncRNA-mediated regulation in response to Symbiodinium infection exhibited in A. digitifera. Once validated, these lncRNAs could be good potential targets for treatment and prevention of bleaching in coral.

Original languageEnglish
Article number48
JournalBMC Genomics
Volume20
Issue number1
DOIs
StatePublished - Jan 16 2019

Bibliographical note

Funding Information:
This work was supported by University of Macau through Research Grants SRG2016–00083-FHS, MYRG2018–00071-FHS, and FHS-CRDA-029-002-2017.

Publisher Copyright:
© 2019 The Author(s).

Keywords

  • Acropora digitifera
  • Alternative splicing
  • Deep RNA-sequencing
  • Long non-coding RNAs
  • Symbiodinium
  • Transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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