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| Status |
Public on Mar 01, 2017 |
| Title |
Selection for transcript diversity in the extremophile Galdieria sulphuraria results in retention of the splicing machinery |
| Organism |
Galdieria sulphuraria |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Red algae show two putative phases of massive genome reduction. RNA-splicing represents an important form of post-transcriptional regulation in eukaryotes. This process generates increased transcriptome and proteome diversity via alternative splicing that can maximize the DNA-encoded genetic diversity embedded within genomes. Why would Spliceosomal Machinery genes and a relatively more complex intron-exon structure be preserved in the compact Galdieria genome? The answer may lie in the fact that RNA-splicing represents an important form of post-transcriptional regulation in eukaryotes. It is hypothesized that his process generates increased transcriptome and proteome diversity via alternative splicing that can maximize the DNA-encoded genetic diversity embedded within genomes.
Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (H-42) and the cultures of G.sulphuraria were swiftly moved to 28°C. After cold treatment at 28°C for 48 hours, a second sampling was performed (C-28.1). The G. sulphuraria was then switched to 46°C for 48 hours, at end of which a third sampling was retrieved (H-46). It again was followed by a cold treatment at 28°C for 48 hours when a fourth sampling was retrieved (C-28.2). Altogether, two 48h timepoints from high temperatures (42°C and 46oC) and two 48h timepoints from cold temperature (28°C) were targeted for sampling.
Results: We show that RNA-splicing provides an avenue for generating transcriptome diversity under strong constraints on genome size and gene number.
Conclusions: We report the relatively high retention of Spliceosomal Machinery genes and the enrichment of intron-exon structures in G. sulphuraria that might be associated with the exceptional transcriptome and proteome diversity of this species. These results suggest that the losses of genes and functions caused by genome reduction might be mitigated by sequence diversity generated by a robust RNA-splicing system. More generally, the strong constraints imposed by genome reduction appear to be ameliorated by processes that operate on the transcriptomic and proteomic levels.
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| Overall design |
mRNA reads of a temperature-shift timecourse were generated by sequencing, using Illumina HiSeq2000, PE-Reads, 2x100bp.
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| Contributor(s) |
Qiu H, Rossoni AW, Weber AP, Yoon HS, Bhattacharya D |
| Citation(s) |
29606099 |
| |
| Submission date |
Oct 25, 2016 |
| Last update date |
May 22, 2019 |
| Contact name |
Andreas PM Weber |
| E-mail(s) |
aweber@hhu.de
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| Organization name |
Heinrich-Heine-University
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| Department |
Institute for Plant Biochemistry
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| Street address |
Universitätsstr. 1
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| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platforms (1) |
| GPL22605 |
Illumina HiSeq 2000 (Galdieria sulphuraria) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA350520 |
| SRA |
SRP092057 |
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