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| Status |
Public on Sep 15, 2014 |
| Title |
Intron evolution in Saccharomycetaceae |
| Organisms |
Saccharomyces cerevisiae; Naumovozyma castellii; Saccharomyces kudriavzevii; Saccharomyces uvarum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Saccharomyceatacea yeast are intron-poor species and they contain on average 300 introns in their genomes. We designed RNAseq experiment to investigate if splicing patterns in related yeast species are similar.
Methods: Total RNA was extracted from wild type cells and processed by the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA. cDNA libraries were prepared according to manufacturer's protocol and sequenced by SOLiD. Sequence reads were filtered and processed by TopHat.
Results: We found 216, 163, 200 and 155 predicted introns with canonical splice signals in S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii respectively. Three introns in S. cerevisiae, four in S. bayanus and ten in S. castellii are novel compared to Saccharomyces Genome Database (SGD) annotations. The expression of introns and splicing shows very high correlation between species.
Conclusion: Transcripts with introns in yeast species tested show similar levels of expression and splicing. We found few novel introns, which are conserved in yeast genomes.
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| Overall design |
Total RNA profiles from wild type yeast S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii generated by RNAseq using SOLiD.
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| Contributor(s) |
Hooks KB, Naseeb S |
| Citation(s) |
25364803 |
| |
| Submission date |
Jun 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Katarzyna B Hooks |
| E-mail(s) |
katarzyna.hooks@gmail.com
|
| Organization name |
Univ. Bordeaux
|
| Department |
CBIB
|
| Street address |
146, rue Léo Saignat
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| City |
Bordeaux |
| ZIP/Postal code |
33076 |
| Country |
France |
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| Platforms (4)
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| GPL15263 |
AB SOLiD 4 System (Saccharomyces cerevisiae) |
| GPL18876 |
AB SOLiD 4 System (Saccharomyces kudriavzevii) |
| GPL18877 |
AB SOLiD 4 System (Saccharomyces uvarum) |
| GPL18878 |
AB SOLiD 4 System (Naumovozyma castellii) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA253808 |
| SRA |
SRP043627 |
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