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| Status |
Public on Aug 20, 2017 |
| Title |
Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals |
| Organism |
Acropora millepora |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Corals are major sources of dimethylsulphoniopropionate (DMSP), a compound that plays a central role in the global sulphur cycle. While DMSP biosynthesis pathways have been investigated in plants and algae, the molecular basis for its production by corals is unknown. Given its potential role as an osmolyte, the effect of salinity stress on levels of DMSP was investigated in both adults and juveniles (lacking photosynthetic symbionts) of the coral Acropora millepora. This study used transcriptomic data to analyse the effects of salinity over the coral A. millepora and to identify coral genes likely to be involved in DMSP biosynthesis.
Methods: Adults coral transcriptomic libraries were constructed from samples exposed during 1 and 24 hours of salinity treatment (25 PSU) and control (35 PSU) conditions (n=5 per condition). Juveniles coral transcriptomic libraries were constructed from samples exposed to 24 and 48 hours of salinity treatment (28 PSU) and control (35 PSU) conditions (n=6 per condition). All libraries were sequenced by 100 bp paired-end in a HiSeq 2000. Reads were mapped onto the Acropora millepora genome using TopHat2 to produce a count data gene expression matrix for subsequent gene expression analysis using DESeq2 package.
Results: In adult coral samples, 5.5 - 10.2 million RNAseq reads were obtained for each treatment sampling time while 3.4 - 8.8 million reads were obtained for each juvenile coral sample. The count matrix of the 26,622 A. millepora gene predictions were generated using htseq-count workflow. BlastP analysis of the A. millepora gene predictions led to the identification of coral members of gene families implicated in DMSP biosynthesis in other organisms, while RNA-seq data was used to identify the differentially expressed ones in response to hyposaline stress and on this basis were considered to be candidates for roles in DMSP biosynthesis in corals.
Conclusions: Hyposaline stress increased DMSP production in both adults and aposymbiotic juvenile corals, and transcriptomic analyses highlighted the potential involvement of specific candidate genes in the production of DMSP via an alga-like pathway. The biochemistry of DMSP production is not well established for any eukaryotic system and, as the first animals in which it has been demonstrated, this is particularly true in the case of corals. Our RNA-seq results enabled the identification of candidates for roles in DMSP biosynthesis in corals but, given its critical roles in diverse biological processes, a thorough investigation of the molecular mechanisms leading to its production by corals is required.
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| Overall design |
RNA-seq profiles of Acropora millepora coral adults (n=18) and juveniles (n=23) under hyposaline stress were generated by 100 bp paired-end sequencing using HiSeq 2000.
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| Contributor(s) |
Aguilar C, Raina J, Motti CA, Fôret S, Hayward D, Lapeyre B, Bourne DG, Miller DJ |
| Citation(s) |
28806970, 30786881 |
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| Submission date |
Mar 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Catalina Aguilar |
| E-mail(s) |
[email protected]
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| Organization name |
James Cook University
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| Department |
Collegue of Public Health, Medical and Veterinary Sciences
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| Lab |
Coral Genomics
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| Street address |
1 James Cook Dr.
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| City |
Townsville |
| State/province |
Queensland |
| ZIP/Postal code |
4811 |
| Country |
Australia |
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| Platforms (1) |
| GPL23215 |
Illumina HiSeq 2000 (Acropora millepora) |
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| Samples (45)
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| Relations |
| BioProject |
PRJNA380267 |
| SRA |
SRP102428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96916_adult_counts_E.csv.gz |
660.4 Kb |
(ftp)(http) |
CSV |
| GSE96916_amil_1.0.maker_006.genes.gff.gz |
4.7 Mb |
(ftp)(http) |
GFF |
| GSE96916_amil_1.0.maker_006.proteins.fasta.gz |
6.7 Mb |
(ftp)(http) |
FASTA |
| GSE96916_amil_1.0.maker_006.transcripts.fasta.gz |
14.2 Mb |
(ftp)(http) |
FASTA |
| GSE96916_planula_counts_E.csv.gz |
710.9 Kb |
(ftp)(http) |
CSV |
| GSE96916_sample_processed_data_header_relationship.txt.gz |
744 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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