Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra.
Convergent evolution
Gnetales
Integument
Model organisms
Ovule
RNAseq
Seed development
Journal
EvoDevo
ISSN: 2041-9139
Titre abrégé: Evodevo
Pays: England
ID NLM: 101525836
Informations de publication
Date de publication:
27 Apr 2022
27 Apr 2022
Historique:
received:
04
09
2021
accepted:
04
04
2022
entrez:
28
4
2022
pubmed:
29
4
2022
medline:
29
4
2022
Statut:
epublish
Résumé
Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development. We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica. This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.
Sections du résumé
BACKGROUND
BACKGROUND
Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development.
RESULTS
RESULTS
We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica.
CONCLUSIONS
CONCLUSIONS
This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.
Identifiants
pubmed: 35477429
doi: 10.1186/s13227-022-00195-4
pii: 10.1186/s13227-022-00195-4
pmc: PMC9047513
doi:
Types de publication
Journal Article
Langues
eng
Pagination
10Informations de copyright
© 2022. The Author(s).
Références
Plant Mol Biol. 2000 Jan;42(1):115-49
pubmed: 10688133
Cell. 1992 Feb 21;68(4):683-97
pubmed: 1346756
Mol Endocrinol. 2005 Mar;19(3):563-73
pubmed: 15677708
Plant J. 2010 Apr;62(2):203-14
pubmed: 20088901
Evol Dev. 2011 Mar-Apr;13(2):171-81
pubmed: 21410873
Plant J. 2013 May;74(4):663-77
pubmed: 23425240
Nature. 1991 Sep 5;353(6339):31-7
pubmed: 1715520
Sci Rep. 2018 Apr 16;8(1):6053
pubmed: 29662101
Mol Biol Evol. 2012 Aug;29(8):2019-29
pubmed: 22337864
Plant Mol Biol. 2009 Sep;71(1-2):1-14
pubmed: 19488678
Curr Opin Plant Biol. 2001 Oct;4(5):447-56
pubmed: 11597504
Genes (Basel). 2021 Jul 30;12(8):
pubmed: 34440362
Plant J. 2015 Jul;83(1):121-32
pubmed: 25762111
Plant J. 2012 May;70(3):409-20
pubmed: 22176531
Syst Biol. 2008 Oct;57(5):758-71
pubmed: 18853362
Curr Opin Cell Biol. 2002 Dec;14(6):692-9
pubmed: 12473341
Nat Methods. 2012 Jul 30;9(8):772
pubmed: 22847109
Biochem Biophys Res Commun. 2002 Jan 25;290(3):998-1009
pubmed: 11798174
Nat Rev Genet. 2003 Nov;4(11):865-75
pubmed: 14634634
Bioinformatics. 2014 Nov 15;30(22):3276-8
pubmed: 25095880
Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7342-7
pubmed: 10377416
Plant J. 2004 Feb;37(4):566-77
pubmed: 14756763
Plant J. 1998 Sep;15(5):615-23
pubmed: 9778844
Evol Dev. 2021 May;23(3):256-266
pubmed: 33503333
Mol Biol Evol. 2012 Jan;29(1):409-19
pubmed: 21972256
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Dev Genet. 1999 Sep;25(3):245-52
pubmed: 10528265
PLoS One. 2012;7(3):e33246
pubmed: 22438902
Trends Genet. 2009 Sep;25(9):414-23
pubmed: 19716619
Chromosoma. 2010 Feb;119(1):27-33
pubmed: 19701762
Plant J. 2006 Jun;46(5):823-33
pubmed: 16709197
Plant Signal Behav. 2010 Jul;5(7):899-902
pubmed: 20484990
PLoS One. 2007 Mar 28;2(3):e324
pubmed: 17389915
Nature. 2000 May 11;405(6783):200-3
pubmed: 10821278
Biochem Soc Trans. 2014 Apr;42(2):358-63
pubmed: 24646244
Plant Cell. 1998 Feb;10(2):135-54
pubmed: 9490739
Bot J Linn Soc. 2010;163(4):387-430
pubmed: 20799438
Mol Genet Genomics. 2002 Feb;266(6):942-50
pubmed: 11862488
Nat Rev Genet. 2011 Aug 31;12(10):692-702
pubmed: 21878963
Front Plant Sci. 2017 May 30;8:895
pubmed: 28611810
Plant J. 2010 Sep;63(6):914-24
pubmed: 20598091
Trends Genet. 2009 Sep;25(9):404-13
pubmed: 19716618
Plant Cell. 2002 Oct;14(10):2463-79
pubmed: 12368498
IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92
pubmed: 26356912
Ann Bot. 2019 Jan 1;123(1):133-143
pubmed: 30137225
Nature. 1999 Nov 25;402(6760):402-4
pubmed: 10586878
Biochimie. 2011 Dec;93(12):2048-53
pubmed: 21798306
J Plant Res. 2014 May;127(3):373-88
pubmed: 24496502
Plant J. 2020 Aug;103(3):980-994
pubmed: 32314448
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Annu Rev Cell Dev Biol. 2005;21:133-53
pubmed: 16212490
Trends Genet. 2003 Nov;19(11):629-39
pubmed: 14585615
Mol Phylogenet Evol. 2020 Jun;147:106786
pubmed: 32135310
Microbiology (Reading). 2005 Aug;151(Pt 8):2499-2501
pubmed: 16079329
Mol Biol Evol. 1996 Feb;13(2):383-96
pubmed: 8587503
Plant Physiol. 2013 Jun;162(2):616-25
pubmed: 23632852
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Ann Bot. 2013 Aug;112(3):535-44
pubmed: 23761686
Methods Mol Biol. 2014;1079:131-46
pubmed: 24170399
Genetics. 1998 Jun;149(2):765-83
pubmed: 9611190
Plant Cell. 2007 Feb;19(2):473-84
pubmed: 17307931
Cell Res. 2015 Jan;25(1):121-34
pubmed: 25378179
Genome Biol. 2010;11(6):214
pubmed: 20587009
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Dev Genes Evol. 2003 Nov;213(11):567-72
pubmed: 14551771
Ann Bot. 2021 Jul 30;128(2):217-230
pubmed: 33959756
BMC Genomics. 2018 Sep 25;19(1):704
pubmed: 30253734
Nature. 1992 Nov 19;360(6401):273-7
pubmed: 1359429
Elife. 2016 Nov 16;5:
pubmed: 27848912
Nat Rev Genet. 2005 Sep;6(9):688-98
pubmed: 16151374
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Plant J. 2006 Sep;47(6):934-46
pubmed: 16925602
Nature. 1990 Jul 5;346(6279):35-9
pubmed: 1973265
Proc Biol Sci. 1994 May 23;256(1346):119-24
pubmed: 8029240
Hortic Res. 2020 Nov 1;7(1):187
pubmed: 33328460
Genome Biol Evol. 2021 Feb 3;13(2):
pubmed: 33196777
New Phytol. 2012 May;194(3):629-646
pubmed: 22432525
Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20826-31
pubmed: 22143805