Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species.
alternative splicing
embryogenesis
evolution
grain development
polyploid
wheat
Journal
Plant biotechnology journal
ISSN: 1467-7652
Titre abrégé: Plant Biotechnol J
Pays: England
ID NLM: 101201889
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
revised:
25
02
2021
received:
15
09
2020
accepted:
08
03
2021
pubmed:
12
3
2021
medline:
4
9
2021
entrez:
11
3
2021
Statut:
ppublish
Résumé
Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat crops are poorly understood. To address this knowledge gap, we developed a pipeline for the analysis of alternatively spliced transcript isoforms, which takes the high sequence similarity among polyploid wheat subgenomes into account. Through analysis of synteny and detection of collinearity of homoeologous subgenomes, conserved and specific AS events across five wheat and grass species were identified. A global analysis of the regulation of AS in diploid grass and polyploid wheat grains revealed diversity in AS events not only between the endosperm, pericarp and embryo overdevelopment, but also between subgenomes. Analysis of AS in homoeologous triads of polyploid wheats revealed evolutionary divergence between gene-level and transcript-level regulation of embryogenesis. Evolutionary age analysis indicated that the generation of novel transcript isoforms has occurred in young genes at a more rapid rate than in ancient genes. These findings, together with the development of comprehensive AS resources for wheat and grass species, advance understanding of the evolution of regulatory features of AS during embryogenesis and grain development in wheat.
Identifiants
pubmed: 33706417
doi: 10.1111/pbi.13579
pmc: PMC8384600
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1624-1643Informations de copyright
© 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Références
Plant Cell. 2019 Dec;31(12):2888-2911
pubmed: 31628162
Science. 2012 Dec 21;338(6114):1587-93
pubmed: 23258890
Nat Genet. 2002 Jan;30(1):29-30
pubmed: 11743582
Plant Biotechnol J. 2018 Mar;16(3):714-726
pubmed: 28834352
Ann Bot. 2016 Apr;117(5):781-94
pubmed: 26346718
Plant Cell. 2013 Oct;25(10):3657-83
pubmed: 24179125
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5593-601
pubmed: 25480548
Nat Protoc. 2016 Sep;11(9):1650-67
pubmed: 27560171
Nature. 2010 Dec 9;468(7325):815-8
pubmed: 21150997
Plant Cell. 1990 Dec;2(12):1201-1224
pubmed: 12354953
Trends Plant Sci. 2016 Jul;21(7):609-621
pubmed: 27021699
Genes Dev. 2007 Nov 15;21(22):2963-75
pubmed: 17978102
New Phytol. 2018 Jan;217(1):163-178
pubmed: 28892169
Int J Mol Sci. 2017 Feb 20;18(2):
pubmed: 28230724
Cell. 2007 Nov 2;131(3):452-62
pubmed: 17981114
Plant Physiol. 2016 Jan;170(1):586-99
pubmed: 26582726
Science. 2012 Dec 21;338(6114):1593-9
pubmed: 23258891
Front Genet. 2014 Feb 12;5:25
pubmed: 24575124
Plant Cell. 2016 Nov;28(11):2715-2734
pubmed: 27803310
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Curr Opin Plant Biol. 2005 Apr;8(2):135-41
pubmed: 15752992
Curr Genomics. 2017 Jun;18(3):268-277
pubmed: 28659722
Plant J. 2011 Apr;66(1):94-116
pubmed: 21443626
Plant Cell. 2018 Jul;30(7):1404-1423
pubmed: 29967286
Theor Appl Genet. 2019 Aug;132(8):2295-2308
pubmed: 31098756
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Plant Cell. 2015 Jan;27(1):71-85
pubmed: 25634987
Plant Biotechnol J. 2021 Aug;19(8):1624-1643
pubmed: 33706417
Genome Biol. 2021 Jan 14;22(1):35
pubmed: 33446251
Front Plant Sci. 2019 Jun 12;10:708
pubmed: 31244866
Plant Cell. 2013 Oct;25(10):3640-56
pubmed: 24179132
Genome Biol. 2018 Mar 23;19(1):40
pubmed: 29571299
Curr Opin Plant Biol. 2010 Apr;13(2):139-45
pubmed: 20064738
Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E913-E921
pubmed: 28096351
Nature. 2010 Jan 28;463(7280):457-63
pubmed: 20110989
Genome Res. 2017 Oct;27(10):1759-1768
pubmed: 28855263
Genome Biol. 2004;5(10):R74
pubmed: 15461793
Cell. 2016 Nov 17;167(5):1170-1187
pubmed: 27863239
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858
pubmed: 30407534
Genetics. 2017 Oct;207(2):465-480
pubmed: 28839042
Plant J. 2004 Sep;39(6):877-85
pubmed: 15341630
Genome Res. 2008 Sep;18(9):1381-92
pubmed: 18669480
Annu Rev Plant Biol. 2007;58:267-94
pubmed: 17222076
Genome Res. 2010 Jan;20(1):45-58
pubmed: 19858364
Science. 2007 Jun 29;316(5833):1862-6
pubmed: 17600208
Nat Genet. 2003 Jun;34(2):177-80
pubmed: 12730695
Nature. 2012 Oct 4;490(7418):98-101
pubmed: 22951968
Plant Physiol. 2020 Dec;184(4):1955-1968
pubmed: 33051269
Bioessays. 2008 Jan;30(1):38-47
pubmed: 18081010
Plant Reprod. 2019 Mar;32(1):93-104
pubmed: 30762127
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W297-9
pubmed: 17485470
Genome Res. 2018 Jun;28(6):921-932
pubmed: 29712755
Science. 2018 Aug 17;361(6403):
pubmed: 30115782