Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
09
02
2023
accepted:
24
07
2023
medline:
25
9
2023
pubmed:
21
9
2023
entrez:
21
9
2023
Statut:
epublish
Résumé
Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.
Identifiants
pubmed: 37733832
doi: 10.1371/journal.pone.0289625
pii: PONE-D-23-03735
pmc: PMC10513226
doi:
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0289625Informations de copyright
Copyright: © 2023 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Mitochondrial DNA B Resour. 2016 Sep 5;1(1):601-602
pubmed: 33473566
Mitochondrial DNA B Resour. 2020 Aug 31;5(3):3284-3285
pubmed: 33458142
Mol Phylogenet Evol. 2019 Jun;135:12-21
pubmed: 30826488
Mol Biol Evol. 2014 Apr;31(4):793-803
pubmed: 24458431
PLoS One. 2017 Aug 1;12(8):e0182281
pubmed: 28763486
Plant Physiol. 2013 Apr;161(4):1918-29
pubmed: 23435694
Mol Biol Evol. 2005 Sep;22(9):1813-22
pubmed: 15930156
Am J Bot. 2012 Mar;99(3):517-28
pubmed: 22334448
Nucleic Acids Res. 2016 Jul 8;44(W1):W54-7
pubmed: 27174935
Mitochondrial DNA B Resour. 2019 Dec 9;5(1):37-38
pubmed: 33366411
Mitochondrial DNA B Resour. 2019 Jul 11;4(2):2291-2292
pubmed: 33365510
Nucleic Acids Res. 2017 Jul 3;45(W1):W6-W11
pubmed: 28486635
Mitochondrial DNA B Resour. 2021 Jan 27;6(1):257-258
pubmed: 33659648
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
pubmed: 15215394
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Front Plant Sci. 2018 Feb 05;9:99
pubmed: 29459880
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
AoB Plants. 2016 Apr 06;8:
pubmed: 26933149
J Biol Chem. 2020 Mar 27;295(13):4134-4170
pubmed: 32060097
Genome Res. 2010 Dec;20(12):1700-10
pubmed: 20978141
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
Mol Phylogenet Evol. 2016 Mar;96:93-101
pubmed: 26724406
PLoS One. 2017 Apr 11;12(4):e0173766
pubmed: 28399123
Bioinformatics. 2017 Aug 15;33(16):2583-2585
pubmed: 28398459
Ecol Evol. 2021 Mar 19;11(9):4158-4171
pubmed: 33976800
Genome Biol. 2016 Jun 23;17(1):134
pubmed: 27339192
Am J Bot. 2018 Jan;105(1):71-84
pubmed: 29532923
PLoS One. 2015 May 12;10(5):e0125332
pubmed: 25966355
Mitochondrial DNA B Resour. 2021 Aug 2;6(9):2538-2540
pubmed: 34377822
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18424-9
pubmed: 19011103
Methods Enzymol. 2005;395:348-84
pubmed: 15865976
Mol Ecol Resour. 2020 Jan;20(1):348-355
pubmed: 31599058
Sci Rep. 2018 Sep 11;8(1):13568
pubmed: 30206286
BMC Plant Biol. 2022 Apr 6;22(1):177
pubmed: 35387599
Ecol Evol. 2019 Jan 21;9(4):1934-1945
pubmed: 30847083
Mitochondrial DNA B Resour. 2017 Dec 21;3(1):36-37
pubmed: 33490485
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
BMC Genomics. 2008 Nov 07;9:533
pubmed: 18992157
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Nucleic Acids Res. 2019 Jul 2;47(W1):W59-W64
pubmed: 30949694
Mitochondrial DNA B Resour. 2020 Sep 1;5(3):3278-3279
pubmed: 33458139
Genomics. 2015 Oct;106(4):221-31
pubmed: 26206079
Plants (Basel). 2021 Feb 19;10(2):
pubmed: 33669616
Plant J. 2005 Oct;44(2):237-44
pubmed: 16212603
Mol Phylogenet Evol. 2015 Jul;88:75-92
pubmed: 25862377
Mitochondrial DNA B Resour. 2018 Jan 24;3(1):137-138
pubmed: 33474096
Front Plant Sci. 2021 Jan 27;11:600354
pubmed: 33584746
Genes (Basel). 2019 Oct 30;10(11):
pubmed: 31671659
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Curr Genet. 2009 Jun;55(3):323-37
pubmed: 19449185
Mol Biol Evol. 2014 Mar;31(3):645-59
pubmed: 24336877
BMC Genomics. 2017 Aug 9;18(1):592
pubmed: 28793854
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Mitochondrial DNA B Resour. 2019 Jul 18;4(2):2537-2538
pubmed: 33365615
Annu Rev Genet. 1985;19:325-54
pubmed: 3936406
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313
Ann Bot. 2007 Sep;100(3):631-40
pubmed: 17428835
Mitochondrial DNA B Resour. 2021 Oct 8;6(11):3171-3173
pubmed: 34746395
Mol Biol Evol. 2013 May;30(5):1188-95
pubmed: 23418397