UM  > Faculty of Health Sciences
Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection
Huang C.; Leng D.; Sun S.; Zhang X.D.
2019
Source PublicationBMC Genomics
ISSN1471-2164
Volume20Issue:1
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. 

KeywordAcropora Digitifera Alternative Splicing Deep Rna-sequencing Long Non-coding Rnas Symbiodinium Transcriptome
DOI10.1186/s12864-019-5429-3
URLView the original
Indexed BySCIE
Language英語English
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000455888500004
The Source to ArticleScopus
Fulltext Access
Citation statistics
Cited Times [WOS]:4   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionFaculty of Health Sciences
Corresponding AuthorZhang X.D.
AffiliationFaculty of Health Sciences, University of Macau, Taipa, Macau
First Author AffilicationFaculty of Health Sciences
Corresponding Author AffilicationFaculty of Health Sciences
Recommended Citation
GB/T 7714
Huang C.,Leng D.,Sun S.,et al. Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection[J]. BMC Genomics,2019,20(1).
APA Huang C.,Leng D.,Sun S.,&Zhang X.D..(2019).Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection.BMC Genomics,20(1).
MLA Huang C.,et al."Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection".BMC Genomics 20.1(2019).
Files in This Item: Download All
File Name/Size Publications Version Access License
2019BMC-Genomics.pdf(3955KB)期刊论文出版稿开放获取CC BY-NC-SAView Download
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Huang C.]'s Articles
[Leng D.]'s Articles
[Sun S.]'s Articles
Baidu academic
Similar articles in Baidu academic
[Huang C.]'s Articles
[Leng D.]'s Articles
[Sun S.]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Huang C.]'s Articles
[Leng D.]'s Articles
[Sun S.]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: 2019BMC-Genomics.pdf
Format: Adobe PDF
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.