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

Content Provider	Springer Nature : BioMed Central
Author	Huang, Chen Leng, Dongliang Sun, Shixue Zhang, Xiaohua Douglas
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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-019-5429-3.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-019-5429-3
Journal	BMC Genomics
Issue Number	1
Volume Number	20
Language	English
Publisher	BioMed Central
Publisher Date	2019-01-16
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Acropora digitifera Symbiodinium Deep RNA-sequencing Transcriptome Alternative splicing Long non-coding RNAs
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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