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Series GSE10515 Query DataSets for GSE10515
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
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
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.
Contributor(s) Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang S, Wu C
Citation(s) 18278047
Submission date Feb 13, 2008
Last update date Mar 19, 2012
Contact name Chung-I Wu
Organization name University of Chicago
Department Ecology and Evoluation
Lab Chung-I Wu Lab
Street address 1101 57th East
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (3)
GPL6196 D. melanogaster Male Head 454 2007
GPL6197 D. simulans Male Head 454 2007
GPL6198 D. pseudoobscura Male Head 454 2007
Samples (3)
GSM246084 D. melanogaster adult male heads 454
GSM246085 D. simulans adult male heads 454
GSM246086 D. pseudoobscura adult male heads 454
BioProject PRJNA107977

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