The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing.
Thrips palmi Karny (Thysanoptera: Thripidae) is the sole vector of Watermelon bud necrosis tospovirus, where the crop loss has been estimated to be around USD 50 million annually. Chemical insecticides are of limited use in the management of T. palmi due to the thigmokinetic behaviour and development of high levels of resistance to insecticides. There is an urgent need to find out an effective futuristic management strategy, where the small RNAs especially microRNAs hold great promise as a key player in the growth and development. miRNAs are a class of short non-coding RNAs involved in regulation of gene expression either by mRNA cleavage or by translational repression. We identified and characterized a total of 77 miRNAs from T. palmi using high-throughput deep sequencing. Functional classifications of the targets for these miRNAs revealed that majority of them are involved in the regulation of transcription and translation, nucleotide binding and signal transduction. We have also validated few of these miRNAs employing stem-loop RT-PCR, qRT-PCR and Northern blot. The present study not only provides an in-depth understanding of the biological and physiological roles of miRNAs in governing gene expression but may also lead as an invaluable tool for the management of thysanopteran insects in the future.
Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India.
K B
http://orcid.org/0000-0003-2959-1345
KB
Rebijith
Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India.
R
R
Asokan
Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India.
H Ranjitha
HR
Hande
Division of Horticultural Science, Indian Council of Agricultural Research, New Delhi, India.
N K
NK
Krishna Kumar
Nature. 2014 Jan 16;505(7483):353-9
24429634
Insect Biochem Mol Biol. 2013 Apr;43(4):398-406
23108205
Genes Brain Behav. 2012 Aug;11(6):660-70
22409512
Nucleic Acids Res. 2005 Nov 27;33(20):e179
16314309
Mol Cell. 2013 Sep 26;51(6):792-806
24035497
Bioinformatics. 2012 Nov 15;28(22):3006-8
22976082
Insect Mol Biol. 2008 Aug;17(4):427-36
18651924
Nat Biotechnol. 2013 Mar;31(3):233-9
23360965
Mol Genet Genomics. 2012 Jul;287(7):555-63
22643909
Nat Rev Mol Cell Biol. 2011 Apr;12(4):246-58
21427766
Curr Opin Genet Dev. 2005 Oct;15(5):563-8
16099643
Cell Res. 2012 Jan;22(1):107-26
21931358
Annu Rev Microbiol. 2010;64:123-41
20477536
Insect Biochem Mol Biol. 2012 Jun;42(6):381-95
22406339
PLoS One. 2012;7(7):e40028
22844398
Development. 2012 Oct;139(19):3543-52
22899845
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9667-72
17535905
Mol Cancer Res. 2006 Apr;4(4):235-46
16603637
Development. 2014 Sep;141(18):3458-71
25183868
Methods. 2001 Dec;25(4):402-8
11846609
PLoS One. 2015 Feb 18;10(2):e0116988
25693181
Genome Res. 2009 Sep;19(9):1639-45
19541911
PLoS One. 2013 Nov 13;8(11):e78787
24236051
Mol Biol Rep. 2012 Oct;39(10):9361-71
22763736
Science. 2004 Jan 2;303(5654):95-8
14631048
Sci Rep. 2013;3:2292
23887392
Curr Opin Cell Biol. 2009 Jun;21(3):452-60
19450959
Science. 2001 Oct 26;294(5543):862-4
11679672
BMC Genomics. 2015 Oct 05;16:740
26438165
Auris Nasus Larynx. 2013 Apr;40(2):143-9
22831895
Nature. 2004 Sep 16;431(7006):350-5
15372042
PLoS One. 2012;7(11):e48579
23173035
Plant J. 2006 Apr;46(2):243-59
16623887
PLoS One. 2015 Oct 06;10(10):e0139771
26440407
Bioinformation. 2010 Sep 20;5(3):132-5
21364793
BMC Genomics. 2011 Jan 26;12:62
21266089
Cell Res. 2005 May;15(5):336-60
15916721
PLoS One. 2013 Apr 19;8(4):e59016
23620723
PLoS Genet. 2012;8(3):e1002578
22457636
J Exp Biol. 2013 Oct 1;216(Pt 19):3724-32
23788711
Mol Cell. 2007 Nov 30;28(4):598-613
18042455
Cell. 2009 Apr 17;137(2):273-82
19379693
PLoS Genet. 2007 Dec;3(12):e215
18085825
Annu Rev Biochem. 2010;79:351-79
20533884
PLoS One. 2012;7(3):e33778
22457788
Nat Rev Genet. 2011 Feb;12(2):99-110
21245828
BMC Genomics. 2012 Mar 06;13:83
22394504
Genome Res. 2009 Jan;19(1):92-105
18955434
Annu Rev Entomol. 2005;50:247-69
15355240
Cell. 1993 Dec 3;75(5):843-54
8252621
BMC Genomics. 2008 Apr 22;9:185
18430245
Clin Chem. 2009 Apr;55(4):611-22
19246619
BMC Biotechnol. 2010 Sep 06;10:64
20815927
Int J Biol Sci. 2013;9(1):1-15
23289012
Annu Rev Phytopathol. 2005;43:459-89
16078892
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
12824340
Insect Mol Biol. 2004 Oct;13(5):459-67
15373804
BMC Genomics. 2010 Feb 10;11 Suppl 1:S6
20158877
Genome Biol. 2004;5(9):R65
15345049
Cell. 2004 Jan 23;116(2):281-97
14744438
Nucleic Acids Res. 2012 Jan;40(1):37-52
21911355
PLoS One. 2009;4(3):e4677
19262741
Genome Res. 2007 Dec;17(12):1865-79
17989255
Acta Pharmacol Sin. 2009 Aug;30(8):1177-85
19654583
BMC Plant Biol. 2011 Jan 10;11:5
21219599
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
17991681
Science. 2001 Oct 26;294(5543):853-8
11679670
BMC Genomics. 2010 Jan 20;11:52
20089182
RNA. 2012 Oct;18(10):1771-82
22875808
Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13499-503
9391054
Cell. 2009 Jan 23;136(2):215-33
19167326
Biochem Biophys Res Commun. 2007 Nov 9;363(1):6-11
17714687
Annu Rev Phytopathol. 1992;30:315-48
18643773
Nat Genet. 2006 Jun;38 Suppl:S25-30
16736021
Genome Res. 2008 Dec;18(12):2024-33
18818371
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
16381832
Science. 2003 Mar 7;299(5612):1540
12624257
Nature. 2004 Nov 11;432(7014):231-5
15531879
Genome Biol. 2003;5(1):R1
14709173
J Mol Biol. 1981 Mar 25;147(1):195-7
7265238
PLoS One. 2008 Jan 02;3(1):e1396
18167555
Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
21037258
Nat Commun. 2012;3:1145
23093182
EMBO Rep. 2011 Feb;12(2):172-7
21212805