Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae).
Divergence time estimation
Hypervariable region
Lauraceae
Plastome
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
08 Sep 2022
08 Sep 2022
Historique:
received:
29
06
2022
accepted:
26
08
2022
entrez:
8
9
2022
pubmed:
9
9
2022
medline:
14
9
2022
Statut:
epublish
Résumé
Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe. Among the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnI This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.
Sections du résumé
BACKGROUND
BACKGROUND
Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe.
RESULTS
RESULTS
Among the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnI
CONCLUSIONS
CONCLUSIONS
This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.
Identifiants
pubmed: 36076185
doi: 10.1186/s12864-022-08855-4
pii: 10.1186/s12864-022-08855-4
pmc: PMC9461114
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
642Subventions
Organisme : Chinese Academy of Sciences
ID : XDB31000000
Organisme : Chinese Academy of Sciences
ID : XDB31000000
Informations de copyright
© 2022. The Author(s).
Références
Mol Biol Evol. 2020 Jan 1;37(1):291-294
pubmed: 31432070
PLoS Biol. 2020 Dec 2;18(12):e3001007
pubmed: 33264284
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12794-7
pubmed: 19666622
Syst Biol. 2011 Jan;60(1):3-15
pubmed: 20952756
BMC Plant Biol. 2022 Apr 12;22(1):195
pubmed: 35413790
Sci Rep. 2015 Feb 12;5:8348
pubmed: 25672218
Mol Phylogenet Evol. 2021 Sep;162:107217
pubmed: 34082129
Front Plant Sci. 2021 Aug 04;12:712064
pubmed: 34421963
Nucleic Acids Res. 2017 Jul 3;45(W1):W6-W11
pubmed: 28486635
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
Am J Bot. 2021 Apr;108(4):664-679
pubmed: 33818757
Am J Bot. 2007 Jan;94(1):42-6
pubmed: 21642206
PLoS Biol. 2015 Aug 18;13(8):e1002224
pubmed: 26284513
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W575-81
pubmed: 23609545
PLoS One. 2006 Dec 20;1:e8
pubmed: 17183712
Bioinformatics. 2009 Jun 1;25(11):1451-2
pubmed: 19346325
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
Mol Ecol Resour. 2009 May;9 Suppl s1:151-63
pubmed: 21564974
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Syst Biol. 2011 Mar;60(2):138-49
pubmed: 21248369
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Front Plant Sci. 2021 Sep 24;12:723622
pubmed: 34630471
Bioinformatics. 2017 Aug 15;33(16):2583-2585
pubmed: 28398459
Plant Divers. 2021 Dec 14;44(4):377-388
pubmed: 35967258
Plant Cell. 2018 Nov;30(11):2677-2703
pubmed: 30309901
Bioinformatics. 2018 Sep 1;34(17):3030-3031
pubmed: 29659705
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol Evol. 2017 Sep 1;9(9):2354-2364
pubmed: 28957463
Mol Biol Evol. 2002 Jun;19(6):908-17
pubmed: 12032247
PeerJ. 2020 Oct 15;8:e10155
pubmed: 33088627
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Planta. 2018 Jan;247(1):255-266
pubmed: 28956160
Nat Commun. 2022 Mar 14;13(1):1320
pubmed: 35288565
Nature. 2018 Feb 8;554(7691):234-238
pubmed: 29420476
Sci Rep. 2022 Jan 21;12(1):1120
pubmed: 35064146
BMC Evol Biol. 2008 Jan 31;8:36
pubmed: 18237435
Trends Ecol Evol. 2015 Jan;30(1):25-35
pubmed: 25468359
Mol Phylogenet Evol. 2016 Mar;96:33-44
pubmed: 26718058
PLoS One. 2015 Jul 14;10(7):e0132091
pubmed: 26173113
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Mol Phylogenet Evol. 2014 Aug;77:147-58
pubmed: 24780751
PeerJ. 2017 Sep 18;5:e3820
pubmed: 28948105
Biology (Basel). 2021 May 01;10(5):
pubmed: 34062846
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Plant J. 2000 Apr;22(2):97-104
pubmed: 10792825
Nucleic Acids Res. 2017 Feb 28;45(4):e18
pubmed: 28204566
PLoS Comput Biol. 2014 Apr 10;10(4):e1003537
pubmed: 24722319
Proc Biol Sci. 2022 Jan 12;289(1966):20211308
pubmed: 34982948
Mol Phylogenet Evol. 2020 Oct;151:106901
pubmed: 32619568
Plant J. 2021 Aug;107(3):861-875
pubmed: 34021942
PeerJ. 2016 Jan 28;4:e1660
pubmed: 26835189
New Phytol. 2017 Apr;214(2):842-851
pubmed: 27991660
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
BMC Evol Biol. 2007 May 11;7:73
pubmed: 17498284
Syst Biol. 2021 Jan 1;70(1):162-180
pubmed: 32617587
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Gene. 2020 Mar 30;732:144355
pubmed: 31935501
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Mol Biol Evol. 2014 Mar;31(3):645-59
pubmed: 24336877
Trends Ecol Evol. 2007 May;22(5):258-65
pubmed: 17300853
Front Plant Sci. 2022 Jan 10;12:774482
pubmed: 35082807
Mol Gen Genet. 1996 Aug 27;252(1-2):195-206
pubmed: 8804393
Mol Phylogenet Evol. 2021 Jun;159:107110
pubmed: 33609709
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313