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| Status |
Public on Feb 14, 2008 |
| Title |
The birth and death of microRNA genes in Drosophila |
| Organisms |
Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are small, endogenously expressed RNAs
that regulate mRNAs post-transcriptionally. The class of miRNA
genes, like other gene classes, should experience birth, death
and persistence of its members. We carried out deep
sequencing of miRNAs from three species of Drosophila, and
obtained 107,000 sequences that map to no fewer than 300
loci that were not previously known. We observe a large class
of miRNA genes that are evolutionarily young, with a rate of
birth of 12 new genes per million years (Myr). Most of these
new miRNAs originated from non-miRNA sequences. Among
the new genes, we estimate that 96% disappeared quickly in
the course of evolution; only 4% of new miRNA genes were
retained by natural selection. Furthermore, only 60% of these
retained genes became integrated into the transcriptome in the
long run (60 Myr). This small fraction (2.5%) of surviving
miRNAs may later on become moderately or highly expressed.
Our results suggest that there is a high birth rate of new
miRNA genes, accompanied by a comparably high death rate.
The estimated net gain of long-lived miRNA genes, which
is not strongly affected by either the depth or the breadth
(number of tissues) of sequencing, is 0.3 genes per Myr
in Drosophila
Keywords: 454 microRNA deep sequencing
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| Overall design |
Three small RNA samples from male heads of D. melanogaster, D. simulans and D. pseudoobscura were analyzed. The small RNAs were sequenced by 454 technology. After removing the flank adaptor sequences, the inserted sequences greater than 18nt were extracted.
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| Contributor(s) |
Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang S, Wu C |
| Citation(s) |
18278047 |
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| Submission date |
Feb 13, 2008 |
| Last update date |
Mar 19, 2012 |
| Contact name |
Chung-I Wu |
| E-mail(s) |
cw16@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Ecology and Evoluation
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| Lab |
Chung-I Wu Lab
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| Street address |
1101 57th East
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (3) |
| GPL6196 |
D. melanogaster Male Head 454 2007 |
| GPL6197 |
D. simulans Male Head 454 2007 |
| GPL6198 |
D. pseudoobscura Male Head 454 2007 |
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| Samples (3) |
| GSM246084 |
D. melanogaster adult male heads 454 |
| GSM246085 |
D. simulans adult male heads 454 |
| GSM246086 |
D. pseudoobscura adult male heads 454 |
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| Relations |
| BioProject |
PRJNA107977 |
| Supplementary data files not provided |
| Processed data included within Sample table |
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