Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
31 10 2023
31 10 2023
Historique:
received:
01
06
2023
accepted:
19
10
2023
medline:
2
11
2023
pubmed:
1
11
2023
entrez:
1
11
2023
Statut:
epublish
Résumé
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
Identifiants
pubmed: 37907468
doi: 10.1038/s41598-023-45421-8
pii: 10.1038/s41598-023-45421-8
pmc: PMC10618267
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
18731Informations de copyright
© 2023. The Author(s).
Références
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W575-81
pubmed: 23609545
BMC Res Notes. 2016 Feb 12;9:88
pubmed: 26868221
Hortic Res. 2019 Jul 21;6:89
pubmed: 31666958
Mitochondrial DNA B Resour. 2022 Jan 10;7(1):182-184
pubmed: 35028413
Mol Biol Evol. 2002 Dec;19(12):2084-91
pubmed: 12446800
Int J Mol Sci. 2018 Aug 18;19(8):
pubmed: 30126202
Nucleic Acids Res. 2019 Jul 2;47(W1):W65-W73
pubmed: 31066451
Evol Bioinform Online. 2011;7:271-8
pubmed: 22253533
Biomed Res Int. 2019 Jul 15;2019:5190425
pubmed: 31380427
Mol Phylogenet Evol. 1999 Aug;12(3):333-49
pubmed: 10413627
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Hereditas. 2005 Feb;142(2005):24-32
pubmed: 16970608
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
pubmed: 15215394
J Mol Evol. 2002 Nov;55(5):501-8
pubmed: 12399924
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
Genes (Basel). 2022 Jul 01;13(7):
pubmed: 35885967
Mol Biol Evol. 1985 Jan;2(1):13-34
pubmed: 3916708
Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
pubmed: 20451164
Plant Biotechnol J. 2011 Apr;9(3):328-33
pubmed: 20796245
Front Plant Sci. 2017 May 19;8:816
pubmed: 28579999
Genomics. 2021 May;113(3):1438-1447
pubmed: 33744343
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Life (Basel). 2022 Jan 09;12(1):
pubmed: 35054485
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
Plants (Basel). 2020 Nov 18;9(11):
pubmed: 33218207
Plant J. 2006 Apr;46(1):85-94
pubmed: 16553897
Bioinformatics. 2017 Aug 15;33(16):2583-2585
pubmed: 28398459
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
pubmed: 3547335
Genome Biol. 2016 Jun 23;17(1):134
pubmed: 27339192
Bioinformatics. 2018 Sep 1;34(17):3030-3031
pubmed: 29659705
Nat Protoc. 2006;1(5):2320-5
pubmed: 17406474
EMBO J. 1986 Sep;5(9):2043-2049
pubmed: 16453699
PLoS One. 2012;7(4):e35071
pubmed: 22511980
Naturwissenschaften. 2004 Nov;91(11):505-18
pubmed: 15452701
Int J Mol Sci. 2020 May 26;21(11):
pubmed: 32466556
Sci Rep. 2020 Jun 23;10(1):10137
pubmed: 32576920
Mol Phylogenet Evol. 2018 Feb;119:170-181
pubmed: 29175095
PeerJ. 2022 Apr 12;10:e13208
pubmed: 35433122
Nat Biotechnol. 2008 Oct;26(10):1135-45
pubmed: 18846087
PLoS One. 2014 Nov 03;9(11):e110656
pubmed: 25365514
PLoS One. 2022 Jul 19;17(7):e0271633
pubmed: 35853031
PLoS One. 2017 Aug 1;12(8):e0182281
pubmed: 28763486
Front Plant Sci. 2016 Jun 28;7:959
pubmed: 27446185
Plant Mol Biol. 2011 Jul;76(3-5):273-97
pubmed: 21424877
BMC Biol. 2021 Oct 29;19(1):232
pubmed: 34711223
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Int J Biol Macromol. 2020 Jun 1;152:340-348
pubmed: 32109476
Molecules. 2019 Jan 11;24(2):
pubmed: 30641990
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Int J Mol Sci. 2019 Sep 13;20(18):
pubmed: 31540236
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12794-7
pubmed: 19666622
Bioinformatics. 1998;14(9):817-8
pubmed: 9918953
Mol Phylogenet Evol. 2012 Feb;62(2):736-47
pubmed: 22138159
BMC Plant Biol. 2020 Nov 13;20(1):519
pubmed: 33187470
Am J Phys Anthropol. 2008 Nov;137(3):245-55
pubmed: 18500746
BMC Evol Biol. 2014 Jul 07;14:151
pubmed: 25001059
Biol Rev Camb Philos Soc. 2015 Feb;90(1):157-66
pubmed: 24666563
Mitochondrial DNA B Resour. 2019 Oct 18;4(2):3634-3635
pubmed: 33366118
Am J Bot. 2007 Mar;94(3):275-88
pubmed: 21636401
PLoS One. 2013 Aug 23;8(8):e73053
pubmed: 24009730
Sci Rep. 2015 Feb 12;5:8348
pubmed: 25672218
Mol Biol Evol. 2006 Nov;23(11):2175-90
pubmed: 16916942
BMC Biol. 2009 Dec 02;7:84
pubmed: 19954512
New Phytol. 2020 May;226(4):1198-1212
pubmed: 31609470
BMC Evol Biol. 2007 Nov 10;7:218
pubmed: 17996115
Plant Syst Evol. 2015;301:809-832
pubmed: 25620836
BMC Evol Biol. 2006 Oct 04;6:77
pubmed: 17020608
New Phytol. 2010 Apr;186(2):299-317
pubmed: 20180912
J Mol Evol. 1986;24(1-2):1-11
pubmed: 3104608
Front Plant Sci. 2015 Oct 06;6:781
pubmed: 26500659
Mol Biol Evol. 2011 Jul;28(7):2077-86
pubmed: 21289370
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313
PLoS One. 2011;6(6):e20660
pubmed: 21674007
DNA Res. 2010 Feb;17(1):11-22
pubmed: 20007682