Identification of short open reading frames in plant genomes.
genome
plant
ribo-seq
sORFs
small open reading frame
Journal
Frontiers in plant science
ISSN: 1664-462X
Titre abrégé: Front Plant Sci
Pays: Switzerland
ID NLM: 101568200
Informations de publication
Date de publication:
2023
2023
Historique:
received:
17
11
2022
accepted:
26
01
2023
entrez:
6
3
2023
pubmed:
7
3
2023
medline:
7
3
2023
Statut:
epublish
Résumé
The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which sequences the ribosome-protected footprints (RPFs) of the translating mRNAs. However, special attention should be paid to RPFs used to identify sORFs in plants due to their small size (~30 nt) and the high complexity and repetitiveness of the plant genome, particularly for polyploidy species. In this work, we compare different approaches to the identification of plant sORFs, discuss the advantages and disadvantages of each method, and provide a guide for choosing different methods in plant sORF studies.
Identifiants
pubmed: 36875581
doi: 10.3389/fpls.2023.1094715
pmc: PMC9975389
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
1094715Informations de copyright
Copyright © 2023 Feng, Jiang, Yu and Zhou.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
J Proteomics. 2021 Jan 6;230:103965
pubmed: 32891891
J Microbiol. 2015 Sep;53(9):616-22
pubmed: 26310304
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2395-400
pubmed: 23341627
J Exp Bot. 2005 Mar;56(413):1039-47
pubmed: 15710632
EMBO J. 2020 Sep 1;39(17):e104763
pubmed: 32744758
Science. 1994 Apr 15;264(5157):421-4
pubmed: 17836906
Life (Basel). 2021 Jul 16;11(7):
pubmed: 34357073
Brief Bioinform. 2022 Jul 18;23(4):
pubmed: 35698834
Genome Res. 2020 Jul;30(7):985-999
pubmed: 32703885
Nature. 2017 May 25;545(7655):487-490
pubmed: 28514447
Nat Methods. 2016 Feb;13(2):165-70
pubmed: 26657557
Plant Cell. 2016 Oct;28(10):2398-2416
pubmed: 27742800
Nucleic Acids Res. 2018 Jun 1;46(10):e61
pubmed: 29538776
Trends Genet. 2002 Sep;18(9):486
pubmed: 12175810
Nat Struct Mol Biol. 2020 Aug;27(8):717-725
pubmed: 32601440
Front Plant Sci. 2012 Aug 24;3:191
pubmed: 22936940
BMC Biol. 2007 Jul 30;5:32
pubmed: 17663791
Nat Protoc. 2020 Feb;15(2):338-363
pubmed: 31915386
Nucleic Acids Res. 2021 May 7;49(8):4613-4628
pubmed: 33836077
3 Biotech. 2022 Mar;12(3):76
pubmed: 35251879
Rice (N Y). 2014 Dec;7(1):18
pubmed: 26224551
Plant J. 1993 Apr;3(4):573-85
pubmed: 8220464
Plant Cell Environ. 2022 Apr;45(4):1229-1241
pubmed: 35128674
Curr Biol. 2012 Jan 24;22(2):103-12
pubmed: 22244999
BMC Genomics. 2021 Aug 12;22(1):612
pubmed: 34384368
Curr Biol. 2008 May 20;18(10):758-762
pubmed: 18472421
Plant J. 2009 Dec;60(6):1031-42
pubmed: 19754518
Cell Rep. 2014 Sep 11;8(5):1365-79
pubmed: 25159147
Int J Mol Sci. 2020 Aug 28;21(17):
pubmed: 32872304
Plant Methods. 2021 Aug 24;17(1):92
pubmed: 34429136
Nature. 2017 May 25;545(7655):491-494
pubmed: 28514448
Methods Enzymol. 2010;470:119-42
pubmed: 20946809
Nature. 2022 Jun;606(7914):535-541
pubmed: 35676481
Plant Cell. 2016 Oct;28(10):2385-2397
pubmed: 27758893
Genome Res. 2007 May;17(5):632-40
pubmed: 17395691
Plants (Basel). 2021 Mar 01;10(3):
pubmed: 33804539
Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E10018-E10027
pubmed: 29087317
Nucleic Acids Res. 2002 Jan 1;30(1):13-6
pubmed: 11752242
Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12170-12175
pubmed: 30413617
Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7126-E7135
pubmed: 27791167
Plant Physiol. 2019 Sep;181(1):367-380
pubmed: 31248964
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
Nature. 2015 Apr 2;520(7545):90-3
pubmed: 25807486
Brief Bioinform. 2023 Jan 19;24(1):
pubmed: 36611257
Nat Plants. 2022 May;8(5):474-480
pubmed: 35501454
Appl Plant Sci. 2022 Jun 14;10(3):e11484
pubmed: 35774992
Biomedicines. 2021 Dec 22;10(1):
pubmed: 35052693
BMC Genomics. 2008 Jul 31;9:361
pubmed: 18667093
Nat Methods. 2018 May;15(5):363-366
pubmed: 29529017
Curr Biol. 2002 May 14;12(10):849-53
pubmed: 12015123
Nature. 2022 Jun;606(7914):527-534
pubmed: 35676474
Plant Cell. 2016 Oct;28(10):2348-2349
pubmed: 27754877