Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.
BACKGROUND
Post-transcriptional regulation in eukaryotes can be operated through microRNA (miRNAs) mediated gene silencing. MiRNAs are small (18-25 nucleotides) non-coding RNAs that play crucial role in regulation of gene expression in eukaryotes. In insects, miRNAs have been shown to be involved in multiple mechanisms such as embryonic development, tissue differentiation, metamorphosis or circadian rhythm. Insect miRNAs have been identified in different species belonging to five orders: Coleoptera, Diptera, Hymenoptera, Lepidoptera and Orthoptera.


RESULTS
We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 149 miRNAs including 55 conserved and 94 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. Pea aphid microRNA sequences have been posted to miRBase: http://microrna.sanger.ac.uk/sequences/.


CONCLUSIONS
Our study has identified candidates as putative regulators involved in reproductive polyphenism in aphids and opens new avenues for further functional analyses.
Legeai
Fabrice
F
INRA, UMR1099 BiO3P, Domaine de la Motte, F-35653 Le Rheu, France.
Rizk
Guillaume
G
Walsh
Thomas
T
Edwards
Owain
O
Gordon
Karl
K
Lavenier
Dominique
D
Leterme
Nathalie
N
Méreau
Agnès
A
Nicolas
Jacques
J
Tagu
Denis
D
Jaubert-Possamai
Stéphanie
S
D000818:Animals; D001042:Aphids / Q000235:genetics*; D001483:Base Sequence; D020869:Gene Expression Profiling; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics
D035683:MicroRNAs
Mol Plant Microbe Interact. 2008 Jun;21(6):701-8
18624634
Nat Rev Mol Cell Biol. 2009 Feb;10(2):126-39
19165215
Cell Res. 2008 Oct;18(10):985-96
18711447
Genome Res. 2008 Jun;18(6):957-64
18469162
Nat Struct Mol Biol. 2008 Apr;15(4):354-63
18376413
Nat Biotechnol. 2008 Apr;26(4):407-15
18392026
Bioinformatics. 2005 Sep 15;21(18):3610-4
15994192
Genome Res. 2004 Oct;14(10A):1902-10
15364901
PLoS One. 2009;4(3):e4677
19262741
Cell. 2005 Jul 1;121(7):1097-108
15989958
Science. 2002 Sep 13;297(5588):1831
12193644
Insect Biochem Mol Biol. 2007 Oct;37(10):1094-102
17785197
Biochimie. 2007 Oct;89(10):1211-20
17629606
Cell. 2005 Jan 14;120(1):21-4
15652478
Nat Genet. 2008 Mar;40(3):351-5
18278047
Dev Biol. 2002 Apr 1;244(1):170-9
11900466
Cell. 2009 Feb 20;136(4):642-55
19239886
Mol Biol Evol. 2010 May;27(5):979-87
20179251
Curr Biol. 2002 Apr 30;12(9):735-9
12007417
Nucleic Acids Res. 2007;35(20):6953-62
17933784
Cell Cycle. 2007 Dec 15;6(24):3034-5
18075311
Bioinformatics. 2007 Jan 15;23(2):142-9
17105718
Nat Genet. 2005 Jul;37(7):766-70
15965474
Genome Biol. 2007;8(6):R97
17543122
Genes Dev. 2005 Dec 15;19(24):2947-52
16357215
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
17991681
Insect Mol Biol. 2008 Aug;17(4):427-36
18651924
Dev Biol. 2007 Nov 15;311(2):592-602
17936267
FEBS J. 2005 Jan;272(1):59-73
15634332
PLoS Biol. 2010 Feb 23;8(2):e1000313
20186266
Biol Cell. 2008 Aug;100(8):441-51
18627352
Genome Biol. 2009;10(1):R6
19146710
Nat Cell Biol. 2009 Mar;11(3):228-34
19255566
BMC Genomics. 2009 Apr 27;10:195
19397817