MicroRNA Evolution

• D. melanogaster-centric evolution
  • D. melanogaster miRNA conservation and sRNA-seq pileup(permission)
  • D. melanogaster cleaned alignments
  • D. melanogaster miRNAs on a single page
  • MiRNAs and Mirtrons by presense-depth
    • Pan-Drosophilid
    • Sophophoran
    • Melanogaster-subgroup
  • MiRNAs and Mirtrons by arm substitution patterns
    • Pan-Drosophilid
    • Sophophoran
    • Melanogaster-subgroup
  • All mirtrons
  • Dmel miRNAs conserved in worm, rodent or primates (Version 4)
    • [Version 3]
    • [Version 2]
    • [Version 1]
  • Variant Detection in 12-fly Genomes
    • Summary
    • Details
  • Atypical ortholog loss
  • miRNA gain/loss analysis (permission) (Excel Spreadsheet)
  • Coservation & Nucleotide substitution progress (permission)
• D. melanogaster miRNA annotation
  • Known miRNAs
  • Cell-lines miRNAs
  • ITS1 miRNA
  • Hansen et al. 2014 miRdentify predictions
  • 5p tailed mirtrons
• Mammalian miRNA annotation
  • Human miRNAs and mirtrons (mirbase21/hg38)
  • Rhesus macaque miRNAs and mirtrons (mirbase21/rheMac3)
  • Mouse miRNAs and mirtrons (mirbase21/mm10)
  • Rat miRNAs and mirtrons (mirbase21/rn6)
  • Rabbit miRNAs and mirtrons (mirbase21/oryCun2)
  • Pig miRNAs and mirtrons (mirbase21/susScr3)
  • Horse miRNAs and mirtrons (mirbase21/equCab2)
  • Human (hg19) mirtron conservation
  • Mouse (mm9) mirtron conservation
  • Fernandez-Valverde 2015 emiRs
  • Fernandez-Valverde 2015 mirtrons
• Short ORFs from Mackowiak et al. Genome Biology 2015
  • Human (hg19) sORFs
  • Mouse (mm10) sORFs
  • D. melanogaster (dm3) sORFs
  • C. elegans (ce6) sORFs
  • Zebrafish (danRer7) sORFs
• 12 Flies Project
  • Final Alignments per family
  • Final Annotation PDF Packets (updated 10-13-2015)

  Species	Confident	Candidate-Rescued	Candidate
  D. melanogaster	[link]	[link]	[link]
  D. simulans	[link]	[link]	[link]
  D. sechellia	[link]	[link]	[link]
  D. yakuba	[link]	[link]	[link]
  D. erecta	[link]	[link]	[link]
  D. ananassae	[link]	[link]	[link]
  D. pseudoobscura	[link]	[link]	[link]
  D. persimilis	[link]	[link]	[link]
  D. willistoni	[link]	[link]	[link]
  D. virilis	[link]	[link]	[link]
  D. mojavensis	[link]	[link]	[link]
  D. grimshawi	[link]	[link]	[link]

  • 12 Flies Library Summary
  • 12 Flies miRNA prediction (Jaaved's reprocessed webpages)

Species	Jaaved's Mirtrons	Erik's Mirtrons	Mirdeep MiRNAs
D. simulans (droSim2)	[link]	[link]	[link]
D. simulans (droSim3) (Obsolete)			[link]
D. sechellia (droSec2)	[link]	[link]	[link]
D. yakuba (droYak3)	[link]	[link]	[link]
D. erecta (droEre2)	[link]	[link]	[link]
D. ananassae (droAna3)	[link]	[link]	[link]
D. pseudobscura (dp5)	[link]	[link]	[link]
D. persimilis (droPer2)	[link]	[link]	[link]
D. willistoni (droWil2)	[link]	[link]	[link]
D. virilis (droVir3)	[link]	[link]	[link]
D. mojavensis (droMoj3)	[link]	[link]	[link]
D. grimshawi (droGri2)	[link]	[link]	[link]

• mirDeep2 12 flies miRNA predictions (mirDeep's PDFs)

Species	Link
D. simulans (droSim2)	[html] [csv]
D. sechellia (droSec2)	[html] [csv]
D. yakuba (droYak3)	[html] [csv]
D. erecta (droEre3)	[html] [csv]
D. ananassae (droAna4)	[html] [csv]
D. pseudobscura (dp5)	[html] [csv]
D. persimilis (droPer2)	[html] [csv]
D. willistoni (droWil2)	[html] [csv]
D. virilis (droVir4)	[html] [csv]
D. mojavensis (droMoj4)	[html] [csv]
D. grimshawi (droGri3)	[html] [csv]

• Other species miRDeep2 miRNA predictions

Species	Link
Mosquito (aedAeg1)	[html] [csv]
Silkworm (bomMor2)	[html] [csv]
Florida carpenter ants (harSal1)	[html] [csv]
Jerdon's jumping ants (camFlo1)	[html] [csv]
Cattle Tick (rhiMic1)	[html] [csv]
Deer Tick (ixoSca1)	[html] [csv]
Spider Mite (tetUrt1)	[html] [csv]
Sea anemone (nemVec1)	[html]

• miRDeep2 D. melanogaster benchmarking

Scenario	Description	Link
Jumbo	All internal and external libraries from GR Berezikov 2011.	[html] [csv]
celllines_prior (Dec 2012)	(Run ?) Only 49 cell-line libraries spanning 25 cell-lines.	[html] [csv]
jumbo_prior (Dec 2012)	(Run 12/29/2012)	[html] [csv]
jumbo_prior (Feb 2012)	(Run 2/3/2012) same as jumbo but all dmel miRNAs supplied as input	[html] [csv]
noprior_3libs_low	Unaware of miRBase miRNAs. Head, Embryo and Male-body libraries with low read-count.	[html] [csv]
prior_3libs_low	Aware of miRBase miRNAs. Head, Embryo and Male-body libraries with low read-count.	[html] [csv]
prior_3libs_high	Aware of miRBase miRNAs. Head, Embryo and Male-body libraries with high read-count.	[html] [csv]
prior_4libs_ovary_high	Aware of miRBase miRNAs. Head, Embryo, Male-body, and Ovary libraries with high read-count.	[html] [csv]

• Miscellaneous Analysis
  • D. melanogaster clustered miRNAs
    • 310-313 cluster
    • 959-964 cluster
    • 983-984 cluster
    • 985-986 cluster
    • 972-979 cluster

Helpful Links

• Jaaved's UCSC Genome Browser
• Erik Ladewig's webpages
• Adding the Lai Lab track hub

Publication Supplementary Websites

• Mammalian Mirtrons
• Adaptive evolution of D. melanogaster miRNAs
• Drosophila cell-line miRNAs
• Correction of D. melanogaster miRNAs alignments