The Multiverse of Plant Small RNAs: How Can We Explore It?
NGS
bioinformatics tools
data analysis
microRNAs
natsiRNAs
phasiRNAs
plant small RNAs
sRNA-seq
siRNAs
software
tasiRNAs
vsiRNAs
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
02 Apr 2022
02 Apr 2022
Historique:
received:
01
03
2022
revised:
28
03
2022
accepted:
31
03
2022
entrez:
12
4
2022
pubmed:
13
4
2022
medline:
14
4
2022
Statut:
epublish
Résumé
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20-24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes-microRNAs (miRNAs) and small interfering RNAs (siRNAs)-which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.
Identifiants
pubmed: 35409340
pii: ijms23073979
doi: 10.3390/ijms23073979
pmc: PMC8999349
pii:
doi:
Substances chimiques
MicroRNAs
0
RNA, Plant
0
RNA, Small Interfering
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : European Union's Horizon research and innovation programme
ID : SGA-CSA No. 739582 under FPA No. 664620
Références
Nucleic Acids Res. 2022 Jan 7;50(D1):D204-D210
pubmed: 34850127
Annu Rev Phytopathol. 2018 Aug 25;56:581-610
pubmed: 29979927
Curr Biol. 2006 May 9;16(9):939-44
pubmed: 16682356
Biochem Biophys Res Commun. 2007 Mar 9;354(2):585-90
pubmed: 17254555
BMC Bioinformatics. 2017 Jan 11;18(1):26
pubmed: 28077064
Cell Mol Life Sci. 2015 Jan;72(1):87-99
pubmed: 25209320
Annu Rev Plant Biol. 2009;60:43-66
pubmed: 19007329
RNA. 2008 May;14(5):836-43
pubmed: 18356539
Annu Rev Plant Biol. 2019 Apr 29;70:489-525
pubmed: 30848930
PLoS One. 2014 May 12;9(5):e97013
pubmed: 24819114
Plant Cell. 2006 Aug;18(8):2051-65
pubmed: 16861386
PLoS One. 2012;7(1):e29669
pubmed: 22235323
Nucleic Acids Res. 2019 Jan 8;47(D1):D155-D162
pubmed: 30423142
Nat Rev Genet. 2007 Nov;8(11):884-96
pubmed: 17943195
Biochim Biophys Acta. 2008 Nov;1779(11):780-8
pubmed: 18471443
Nat Rev Genet. 2013 Feb;14(2):100-12
pubmed: 23329111
Bioinformatics. 2009 Jan 1;25(1):130-1
pubmed: 19017659
Plant J. 2006 Sep;47(6):841-50
pubmed: 16889646
Nature. 2001 Jan 18;409(6818):363-6
pubmed: 11201747
Cell. 2005 Dec 29;123(7):1279-91
pubmed: 16377568
Plant Cell. 2005 Aug;17(8):2186-203
pubmed: 15994906
BMC Plant Biol. 2008 Feb 29;8:25
pubmed: 18312648
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Genes Dev. 2010 May 15;24(10):1010-21
pubmed: 20478994
Nucleic Acids Res. 2018 Sep 28;46(17):8730-8739
pubmed: 30007348
Cancers (Basel). 2021 Nov 12;13(22):
pubmed: 34830818
BMC Genomics. 2019 Feb 13;20(1):133
pubmed: 30760208
Methods Mol Biol. 2010;592:51-7
pubmed: 19802588
Nucleic Acids Res. 2020 Mar 18;48(5):2258-2270
pubmed: 31943065
Nature. 2004 Sep 16;431(7006):356-63
pubmed: 15372043
Plant Cell. 2010 Apr;22(4):1104-17
pubmed: 20363771
Annu Rev Plant Biol. 2006;57:19-53
pubmed: 16669754
Curr Biol. 2005 Nov 22;15(22):2038-43
pubmed: 16303564
Bioinformatics. 2017 Aug 15;33(16):2446-2454
pubmed: 28407097
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):3275-80
pubmed: 14978267
BMC Mol Biol. 2008 Jan 14;9:6
pubmed: 18194570
RNA Biol. 2021 Nov;18(11):1622-1629
pubmed: 33541212
Brief Bioinform. 2018 May 1;19(3):415-424
pubmed: 28073746
Mol Plant Microbe Interact. 2016 Mar;29(3):165-9
pubmed: 26867095
BMC Bioinformatics. 2021 Feb 1;22(1):37
pubmed: 33522913
Nat Rev Genet. 2005 Jan;6(1):24-35
pubmed: 15630419
BMC Genomics. 2017 Aug 22;18(1):644
pubmed: 28830358
BMC Genomics. 2019 Jun 28;20(1):532
pubmed: 31253093
Ann Bot. 2008 Oct;102(4):509-19
pubmed: 18669574
Virology. 2017 Jan;500:130-138
pubmed: 27825033
Curr Biol. 2006 May 9;16(9):927-32
pubmed: 16682354
Plant Cell. 2012 Sep;24(9):3575-89
pubmed: 23001036
Nature. 2005 Oct 13;437(7061):1022-6
pubmed: 16222298
Mol Cell. 2004 Jun 18;14(6):787-99
pubmed: 15200956
Biosystems. 2011 May-Jun;104(2-3):87-93
pubmed: 21237247
Plant Cell. 2004 Aug;16(8):2001-19
pubmed: 15258262
Bioinformatics. 2014 Jul 15;30(14):2066-7
pubmed: 24632500
Trends Genet. 2008 Jul;24(7):323-7
pubmed: 18514357
Development. 2006 Sep;133(18):3539-47
pubmed: 16914499
BMC Bioinformatics. 2017 Mar 20;18(1):180
pubmed: 28320324
Plant Mol Biol. 2009 Jul;70(4):385-401
pubmed: 19353277
Front Plant Sci. 2015 Dec 16;6:1119
pubmed: 26734029
FEBS Lett. 2008 Aug 6;582(18):2679-84
pubmed: 18619960
Genomics. 2020 Sep;112(5):3201-3206
pubmed: 32380232
Plant Cell. 2005 May;17(5):1360-75
pubmed: 15829600
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
pubmed: 12824340
J Biol Res (Thessalon). 2018 Jun 15;25:11
pubmed: 29946534
Nucleic Acids Res. 2019 Jul 2;47(W1):W530-W535
pubmed: 31114926
Genomics Proteomics Bioinformatics. 2018 Apr;16(2):144-151
pubmed: 29730207
Dev Cell. 2007 Jul;13(1):115-25
pubmed: 17609114
Plant Cell. 2008 May;20(5):1231-43
pubmed: 18492871
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9
pubmed: 21622958
Genes (Basel). 2020 Jun 18;11(6):
pubmed: 32570706
Nucleic Acids Res. 2014 Apr;42(8):5270-9
pubmed: 24561804
Plant Sci. 2018 Sep;274:193-200
pubmed: 30080603
Bioinformatics. 2019 Jul 15;35(14):2521-2522
pubmed: 30521000
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8
pubmed: 22693224
Scientifica (Cairo). 2013;2013:783253
pubmed: 24278785
Genomics. 2020 Sep;112(5):3382-3395
pubmed: 32561347
Microbiol Mol Biol Rev. 2003 Dec;67(4):657-85
pubmed: 14665679
Nat Genet. 2007 Jun;39(6):787-91
pubmed: 17486095
Curr Biol. 2008 May 20;18(10):758-762
pubmed: 18472421
J Exp Bot. 2011 Jun;62(10):3563-73
pubmed: 21362738
Nucleic Acids Res. 2017 Dec 1;45(21):12140-12151
pubmed: 29069500
J Exp Bot. 2010;61(1):165-77
pubmed: 19815687
Plant Cell. 2014 Apr 11;26(4):1764-1780
pubmed: 24728648
Genes Dev. 2006 Dec 1;20(23):3255-68
pubmed: 17158744
Plant Physiol. 2012 Oct;160(2):990-9
pubmed: 22846193
Bioinformatics. 2018 Apr 1;34(7):1108-1115
pubmed: 29136092
Science. 2005 Sep 2;309(5740):1519-24
pubmed: 16141061
Plant Cell. 2013 Dec;25(12):4845-62
pubmed: 24368797
NAR Genom Bioinform. 2021 Jul 21;3(3):lqab068
pubmed: 34308351
Plant J. 2007 Dec;52(6):1131-9
pubmed: 17944812
Nature. 1998 Feb 19;391(6669):806-11
pubmed: 9486653
Annu Rev Plant Biol. 2013;64:137-59
pubmed: 23330790
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Mol Syst Biol. 2007;3:103
pubmed: 17437028
Genes (Basel). 2021 Aug 21;12(8):
pubmed: 34440454
Nucleic Acids Res. 2011 Apr;39(7):2821-33
pubmed: 21113019
Plant Cell. 2013 Jul;25(7):2400-15
pubmed: 23881411
BMC Genomics. 2012 Jul 16;13:310
pubmed: 22799740
Methods Mol Biol. 2019;1932:89-97
pubmed: 30701493
Plant Cell. 2006 Nov;18(11):2929-45
pubmed: 17098808
PLoS Genet. 2018 Apr 19;14(4):e1007337
pubmed: 29672610
Nucleic Acids Res. 2014 Oct;42(18):e139
pubmed: 25120269
PLoS Biol. 2004 May;2(5):E104
pubmed: 15024409
J Exp Bot. 2004 Feb;55(396):285-93
pubmed: 14718495
Trends Plant Sci. 2008 Jul;13(7):368-74
pubmed: 18501663
Nature. 2003 Sep 18;425(6955):257-63
pubmed: 12931144
J Plant Physiol. 2009 Dec 15;166(18):2046-57
pubmed: 19628301
Plant Cell. 2016 Feb;28(2):272-85
pubmed: 26869699
Nat Plants. 2017 Jun 30;3:17077
pubmed: 28665396
Plant Physiol. 2017 Aug;174(4):2469-2486
pubmed: 28663332
Nature. 2018 Jan 3;553(7686):82-85
pubmed: 29300014
Genes Dev. 2001 Aug 15;15(16):2122-33
pubmed: 11511543
Plant J. 2008 Jul;55(1):131-51
pubmed: 18363789
Methods. 2014 May 1;67(1):84-90
pubmed: 23810899
Plant Physiol. 2006 Jul;141(3):988-99
pubmed: 16679424
Trends Plant Sci. 2017 Dec;22(12):1056-1068
pubmed: 29032035
Plant J. 2008 Jul;55(1):65-76
pubmed: 18346190
Mol Cell. 2010 May 14;38(3):465-75
pubmed: 20381393
Brief Bioinform. 2021 Jan 18;22(1):463-473
pubmed: 31885040
Genes Dev. 2011 Dec 1;25(23):2540-53
pubmed: 22156213
Plant J. 2015 Aug;83(3):451-65
pubmed: 26042408
EMBO Rep. 2006 Oct;7(10):1052-8
pubmed: 16977334
Nat Rev Genet. 2005 May;6(5):351-60
pubmed: 15861207
Bioinformatics. 2018 Aug 1;34(15):2670-2672
pubmed: 29554210
Science. 1999 Oct 29;286(5441):950-2
pubmed: 10542148
Trends Plant Sci. 2013 Nov;18(11):601-10
pubmed: 23993483
Genomics Proteomics Bioinformatics. 2021 Jul 28;:
pubmed: 34332120
BMC Plant Biol. 2010 Jun 24;10:123
pubmed: 20573268
Trends Cell Biol. 2004 Apr;14(4):156-9
pubmed: 15134074
Bioinformatics. 2018 May 1;34(9):1574-1576
pubmed: 29236948
Nat Biotechnol. 2008 Aug;26(8):941-6
pubmed: 18542052
Development. 2004 Jul;131(14):3357-65
pubmed: 15226253
Plant Cell. 2012 Dec;24(12):4837-49
pubmed: 23263766
Plant Cell Physiol. 2020 Jun 1;61(6):1204-1212
pubmed: 32181856
Plant Cell. 2005 Aug;17(8):2204-16
pubmed: 16006581
Virology. 2015 May;479-480:85-103
pubmed: 25766638
FEBS Lett. 2017 Aug;591(15):2261-2268
pubmed: 28686301
Cell. 2009 Aug 21;138(4):750-9
pubmed: 19703400
J Exp Bot. 2010 Oct;61(15):4157-68
pubmed: 20729483
Bioinformatics. 2020 Dec 30;36(Suppl_2):i618-i624
pubmed: 33381847
Genome Biol. 2012 Jun 15;13(6):R47
pubmed: 22704043
Nucleic Acids Res. 2017 Dec 1;45(21):e177
pubmed: 29036314
Dev Cell. 2005 Apr;8(4):517-27
pubmed: 15809034
Genes Dev. 2007 Dec 1;21(23):3123-34
pubmed: 18003861
Cells. 2021 Jul 13;10(7):
pubmed: 34359940
Curr Biol. 2002 Sep 3;12(17):1484-95
pubmed: 12225663
Mol Biol Evol. 2015 Nov;32(11):2905-18
pubmed: 26318183
Nucleic Acids Res. 2020 Jul 9;48(12):6481-6490
pubmed: 32463462
J Biol Chem. 2007 Jun 1;282(22):16369-78
pubmed: 17405879
Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
pubmed: 21037258
Development. 2004 Sep;131(17):4311-22
pubmed: 15294871
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):18002-7
pubmed: 17071740
Front Plant Sci. 2017 Mar 21;8:322
pubmed: 28377776
Plant Cell. 2015 Mar;27(3):546-62
pubmed: 25747880