Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
18
12
2018
accepted:
27
03
2019
entrez:
16
4
2019
pubmed:
16
4
2019
medline:
8
1
2020
Statut:
epublish
Résumé
Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.
Identifiants
pubmed: 30986259
doi: 10.1371/journal.pone.0215165
pii: PONE-D-18-36060
pmc: PMC6464174
doi:
Substances chimiques
MicroRNAs
0
Plant Proteins
0
RNA, Plant
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0215165Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
J Nat Med. 2013 Jan;67(1):159-67
pubmed: 22484604
Ann Bot. 2012 Sep;110(4):923-34
pubmed: 22778149
Bioimpacts. 2011;1(4):229-35
pubmed: 23678433
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
pubmed: 16381832
Plant Mol Biol. 1999 May;40(1):121-31
pubmed: 10394951
Genomics Proteomics Bioinformatics. 2010 Jun;8(2):113-21
pubmed: 20691396
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
PLoS One. 2015 Jun 22;10(6):e0129422
pubmed: 26098898
Plant J. 2015 Jun;82(6):951-961
pubmed: 25912611
Cell Mol Life Sci. 2006 Jan;63(2):246-54
pubmed: 16395542
Plant Cell Physiol. 1995 Jan;36(1):29-36
pubmed: 7719631
Plant J. 2006 Aug;47(4):547-63
pubmed: 16813579
J Biol Chem. 1994 Oct 28;269(43):26684-90
pubmed: 7929401
Genet Mol Res. 2016 Jan 29;15(1):
pubmed: 26909943
Front Genet. 2014 Jun 25;5:190
pubmed: 25009556
BMC Genomics. 2017 May 25;18(1):409
pubmed: 28545396
Methods Mol Biol. 2000;132:365-86
pubmed: 10547847
Phytochemistry. 2003 Sep;64(1):177-86
pubmed: 12946416
Plant Mol Biol. 1993 Jan;21(2):385-9
pubmed: 8425063
Food Chem Toxicol. 2008 May;46(5):1474-87
pubmed: 18215450
Eur J Biochem. 1995 Oct 1;233(1):132-9
pubmed: 7588736
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Toxicol Lett. 2011 Jun 10;203(2):135-41
pubmed: 21419197
Plant Cell. 2010 Oct;22(10):3489-503
pubmed: 21037103
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
PLoS One. 2015 Nov 16;10(11):e0143017
pubmed: 26571372
Plant J. 2004 Oct;40(2):302-13
pubmed: 15447655
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
pubmed: 16845012
Plant Cell Physiol. 2015 May;56(5):1019-30
pubmed: 25713177
PLoS One. 2013;8(1):e53409
pubmed: 23326424
Biochim Biophys Acta. 2012 Feb;1819(2):86-96
pubmed: 21867785
PeerJ. 2017 Jun 15;5:e3422
pubmed: 28630801
Plant J. 1998 Mar;13(6):793-801
pubmed: 9681018
Front Plant Sci. 2016 Feb 16;7:98
pubmed: 26909086
Genome Res. 2016 Aug;26(8):1134-44
pubmed: 27252236
BMC Genomics. 2010 Feb 08;11:94
pubmed: 20141623
BMC Plant Biol. 2015 Sep 18;15:227
pubmed: 26384972
J Biol Chem. 2002 Jan 4;277(1):830-5
pubmed: 11682473
Nat Methods. 2011 Sep 29;8(10):785-6
pubmed: 21959131
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
Phytochemistry. 2000 Mar;53(5):555-64
pubmed: 10724180
Nat Prod Res. 2011 May;25(9):863-75
pubmed: 21491327
Plant J. 2014 Jan;77(2):173-84
pubmed: 24708518
Bioorg Med Chem Lett. 2011 Dec 1;21(23):6960-3
pubmed: 22024033
Plant Cell Physiol. 2007 Jan;48(1):8-18
pubmed: 17132631
Front Plant Sci. 2016 Aug 17;7:1203
pubmed: 27582746
J Sep Sci. 2010 Apr;33(8):1004-9
pubmed: 20183823
Syst Biol. 2012 Dec 1;61(6):1061-7
pubmed: 22780991
Dev Cell. 2007 Jul;13(1):115-25
pubmed: 17609114
Front Plant Sci. 2012 Sep 25;3:220
pubmed: 23056003
Funct Plant Biol. 2012 Sep;39(9):736-744
pubmed: 32480824
Genome Res. 2008 May;18(5):821-9
pubmed: 18349386
Genome Biol. 2010;11(3):R25
pubmed: 20196867
J Exp Bot. 2008;59(6):1201-13
pubmed: 18359753
Sci Rep. 2016 Mar 03;6:22456
pubmed: 26936416
Planta. 2001 Oct;213(6):898-906
pubmed: 11722126
Nature. 2002 Sep 12;419(6903):167-70
pubmed: 12226665
J Biol Chem. 2003 Oct 3;278(40):38557-65
pubmed: 12732624
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Genome Biol. 2015 Feb 11;16:30
pubmed: 25723335
J Exp Bot. 2014 Jul;65(14):4009-22
pubmed: 24567495
Biol Pharm Bull. 2012;35(5):666-71
pubmed: 22687399
Plant Cell. 2010 Oct;22(10):3390-409
pubmed: 20959558
Trends Plant Sci. 2004 Dec;9(12):591-6
pubmed: 15564126
Planta. 2016 Nov;244(5):1055-1064
pubmed: 27401454
Bioinformatics. 2017 Feb 1;33(3):327-333
pubmed: 28172640
Curr Opin Struct Biol. 2004 Jun;14(3):283-91
pubmed: 15193307
J Biotechnol. 2013 Jul 10;166(3):122-34
pubmed: 23602801
PLoS Genet. 2012 Jan;8(1):e1002419
pubmed: 22242012
Antiviral Res. 2006 Nov;72(2):153-6
pubmed: 16647765
Mol Biol Evol. 2003 May;20(5):735-47
pubmed: 12679534
Bioinformatics. 2012 Apr 15;28(8):1086-92
pubmed: 22368243
BMC Genomics. 2011 Sep 19;12:451
pubmed: 21929789
Bioinformatics. 2013 Jul 01;29(13):i326-34
pubmed: 23813001
J Plant Physiol. 2012 Mar 15;169(5):509-15
pubmed: 22297127
J Biol Chem. 2002 Sep 13;277(37):33878-83
pubmed: 12107162
Phytochemistry. 2005 Oct;66(20):2501-20
pubmed: 16342378
Front Plant Sci. 2016 Jan 28;6:1199
pubmed: 26858723
Plant Cell Physiol. 2011 Jul;52(7):1131-41
pubmed: 21576193
J Mol Biol. 2001 Jan 19;305(3):567-80
pubmed: 11152613
Forsch Komplementmed. 2010 Oct;17(5):241-8
pubmed: 20980763
Plant Signal Behav. 2011 Oct;6(10):1609-11
pubmed: 21957499
Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
pubmed: 22127870
J Biol Chem. 2007 May 18;282(20):14741-51
pubmed: 17389594
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
PLoS One. 2013 Apr 23;8(4):e62293
pubmed: 23626799
J Exp Bot. 2011 May;62(8):2465-83
pubmed: 21278228
Theor Appl Genet. 2003 Feb;106(3):411-22
pubmed: 12589540
Molecules. 2013 Aug 29;18(9):10413-24
pubmed: 23994968
BMC Genomics. 2013 Jul 09;14:465
pubmed: 23837739
PLoS One. 2012;7(6):e38653
pubmed: 22723874
PLoS Comput Biol. 2016 Feb 19;12(2):e1004772
pubmed: 26894997
Plant Cell. 2004 Nov;16(11):3033-44
pubmed: 15486100
Genome Biol. 2015 Aug 06;16:157
pubmed: 26243257
Nucleic Acids Res. 2014 Jan;42(Database issue):D1182-7
pubmed: 24174544
BMC Bioinformatics. 2012 Jul 18;13:170
pubmed: 22808927
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nat Prod Commun. 2010 Nov;5(11):1751-4
pubmed: 21213973