Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement.
Aegilops
Sitopsis
annotation
genome sequence
haplotype
nucleotide-binding leucine-rich repeat (NLR)
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
04 2022
04 2022
Historique:
revised:
21
12
2021
received:
12
11
2021
accepted:
03
01
2022
pubmed:
9
1
2022
medline:
6
4
2022
entrez:
8
1
2022
Statut:
ppublish
Résumé
Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.
Identifiants
pubmed: 34997796
doi: 10.1111/tpj.15664
pmc: PMC10138734
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
179-192Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/J/000PR9780
Pays : United Kingdom
Informations de copyright
© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.
Références
Theor Appl Genet. 2005 Mar;110(5):859-64
pubmed: 15690175
Am J Bot. 2005 Nov;92(11):1887-98
pubmed: 21646106
Plant Dis. 2007 Aug;91(8):942-950
pubmed: 30780426
Mol Phylogenet Evol. 2006 Apr;39(1):70-82
pubmed: 16504543
Mol Phylogenet Evol. 2019 Oct;139:106554
pubmed: 31288105
Nat Biotechnol. 2022 Mar;40(3):422-431
pubmed: 34725503
Science. 2018 Aug 17;361(6403):
pubmed: 30115783
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Genome. 1996 Apr;39(2):293-306
pubmed: 18469894
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
Plant Genome. 2017 Nov;10(3):
pubmed: 29293809
Genome. 1996 Dec;39(6):1150-8
pubmed: 18469963
Plant Cell. 2018 Feb;30(2):285-299
pubmed: 29382771
Nat Biotechnol. 2021 May;39(5):561-566
pubmed: 33398152
Annu Rev Genet. 2017 Nov 27;51:435-454
pubmed: 28934591
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Nature. 2020 Dec;588(7837):277-283
pubmed: 33239791
BMC Plant Biol. 2020 Apr 9;20(1):153
pubmed: 32272895
Front Plant Sci. 2019 May 09;10:585
pubmed: 31143197
Sci Data. 2017 Apr 27;4:170044
pubmed: 28448065
Nat Biotechnol. 2019 Feb;37(2):139-143
pubmed: 30718880
Cell. 2019 Aug 22;178(5):1260-1272.e14
pubmed: 31442410
Trends Plant Sci. 2021 Jul;26(7):677-684
pubmed: 33612402
Genome. 2014 Jun;57(6):309-16
pubmed: 25209724
Science. 2014 Jul 18;345(6194):1251788
pubmed: 25035500
Genome Biol. 2019 Dec 18;20(1):284
pubmed: 31849336
New Phytol. 2013 May;198(3):925-937
pubmed: 23374069
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66
pubmed: 14500829
Science. 2014 Jul 18;345(6194):1250092
pubmed: 25035499
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Nat Genet. 2020 Dec;52(12):1412-1422
pubmed: 33106631
Plant Dis. 2014 Oct;98(10):1309-1320
pubmed: 30703930
Nat Genet. 2019 May;51(5):885-895
pubmed: 30962619
Sci Adv. 2019 May 01;5(5):eaav9188
pubmed: 31049399
Theor Appl Genet. 2017 Jun;130(6):1207-1222
pubmed: 28275817
Commun Biol. 2020 Nov 25;3(1):712
pubmed: 33239669
Nucleic Acids Res. 2002 Jun 1;30(11):2478-83
pubmed: 12034836
Curr Protoc Bioinformatics. 2019 Mar;65(1):e57
pubmed: 30466165
Plant Dis. 2018 Jun;102(6):1124-1135
pubmed: 30673435
BMC Bioinformatics. 2006 Feb 09;7:62
pubmed: 16469098
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Science. 2017 Jul 7;357(6346):93-97
pubmed: 28684525
Mol Plant. 2021 Jul 5;14(7):1053-1070
pubmed: 33991673
Nat Genet. 2019 May;51(5):905-911
pubmed: 31043760
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Nature. 2017 Nov 23;551(7681):498-502
pubmed: 29143815
Plant J. 2020 May;102(3):493-506
pubmed: 31821649
Science. 2007 Jun 29;316(5833):1862-6
pubmed: 17600208
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Sci Rep. 2018 Nov 6;8(1):16397
pubmed: 30401925
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Theor Appl Genet. 2006 May;112(8):1563-72
pubmed: 16568284
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Genome. 2008 Aug;51(8):616-27
pubmed: 18650951
Methods Mol Biol. 2016;1374:339-61
pubmed: 26519415
Theor Appl Genet. 2021 Aug;134(8):2469-2479
pubmed: 33987716
Plant Dis. 2005 Mar;89(3):303-308
pubmed: 30795354
Plant Physiol. 2020 Jun;183(2):468-482
pubmed: 32184345