Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications.
Liverworts
Marchantiophyta
evolution
gene duplication
phylogeny
transcriptome
Journal
Annals of botany
ISSN: 1095-8290
Titre abrégé: Ann Bot
Pays: England
ID NLM: 0372347
Informations de publication
Date de publication:
31 Dec 2022
31 Dec 2022
Historique:
received:
24
05
2022
accepted:
08
09
2022
pubmed:
9
9
2022
medline:
24
1
2023
entrez:
8
9
2022
Statut:
ppublish
Résumé
With some 7300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole-genome duplications, are still contentious. Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55 taxon liverwort species tree. Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole-genome duplication events along the backbone phylogeny of liverworts. With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole-genome duplication during the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole-genome duplications.
Sections du résumé
BACKGROUND AND AIMS
OBJECTIVE
With some 7300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole-genome duplications, are still contentious.
METHODS
METHODS
Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55 taxon liverwort species tree.
KEY RESULTS
RESULTS
Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole-genome duplication events along the backbone phylogeny of liverworts.
CONCLUSIONS
CONCLUSIONS
With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole-genome duplication during the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole-genome duplications.
Identifiants
pubmed: 36075207
pii: 6694240
doi: 10.1093/aob/mcac113
pmc: PMC9851303
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
951-964Subventions
Organisme : Scientific Foundation of the Urban Management Bureau of Shenzhen
ID : 202106
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Références
Nature. 2019 Oct;574(7780):679-685
pubmed: 31645766
Bioinformatics. 2014 Sep 1;30(17):i541-8
pubmed: 25161245
Cladistics. 2018 Oct;34(5):517-541
pubmed: 34706484
Nat Commun. 2019 Apr 2;10(1):1485
pubmed: 30940807
IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):517-35
pubmed: 21233529
Plant J. 2018 Feb;93(3):515-533
pubmed: 29237241
Bioinformatics. 2010 Apr 1;26(7):962-3
pubmed: 20156990
Mol Plant. 2020 Jan 6;13(1):59-71
pubmed: 31678615
Mol Biol Evol. 2016 Jul;33(7):1654-68
pubmed: 27189547
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Cladistics. 2020 Apr;36(2):184-193
pubmed: 34618956
Mol Biol Evol. 1994 Sep;11(5):715-24
pubmed: 7968485
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Curr Biol. 2020 Jun 8;30(11):2001-2012.e2
pubmed: 32302587
Syst Biol. 2007 Aug;56(4):564-77
pubmed: 17654362
BMC Evol Biol. 2015 Aug 05;15:150
pubmed: 26239519
New Phytol. 2016 May;210(3):1121-9
pubmed: 27074401
J Mol Evol. 2008 Apr;66(4):350-61
pubmed: 18330485
Genome Biol. 2012 Jan 26;13(1):R3
pubmed: 22280555
New Phytol. 2016 Mar;209(4):1734-46
pubmed: 26505145
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Plants. 2020 Feb;6(2):107-118
pubmed: 32042158
BMC Evol Biol. 2018 Feb 2;18(1):11
pubmed: 29390973
Cladistics. 2021 Jun;37(3):231-247
pubmed: 34478198
Mol Biol Evol. 2021 Jun 25;38(7):2750-2766
pubmed: 33681996
Cladistics. 2022 Feb;38(1):126-146
pubmed: 35049082
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Nat Plants. 2020 Mar;6(3):215-222
pubmed: 32094642
Cell. 2017 Oct 5;171(2):287-304.e15
pubmed: 28985561
BMC Biol. 2013 Apr 15;11:29
pubmed: 23587068
Nat Rev Genet. 2017 Jul;18(7):411-424
pubmed: 28502977
Bioinformatics. 2019 Jun 1;35(12):2153-2155
pubmed: 30398564
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
pubmed: 16845082
Philos Trans R Soc Lond B Biol Sci. 2000 Jun 29;355(1398):815-30; discussion 830-1
pubmed: 10905611
Syst Biol. 2012 Oct;61(5):727-44
pubmed: 22605266
Plant Cell. 2022 Jul 4;34(7):2466-2474
pubmed: 35253876
Commun Biol. 2018 Oct 19;1:169
pubmed: 30374461
Curr Opin Plant Biol. 2012 Apr;15(2):147-53
pubmed: 22480429
PLoS One. 2016 Oct 5;11(10):e0163962
pubmed: 27706213
Mol Plant. 2018 Mar 5;11(3):414-428
pubmed: 29317285
Plant J. 2021 Mar;105(5):1339-1356
pubmed: 33277766
Syst Biol. 2014 Nov;63(6):862-78
pubmed: 25070972
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Mol Phylogenet Evol. 2021 May;158:107083
pubmed: 33516804
Nature. 2011 May 5;473(7345):97-100
pubmed: 21478875
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2274-E2283
pubmed: 29463716
Genome Biol. 2007;8(6):R109
pubmed: 17567924
New Phytol. 2018 Jun;218(4):1668-1684
pubmed: 29604235
Mol Biol Evol. 2021 Jul 29;38(8):3332-3344
pubmed: 33871608
Bioinformatics. 2006 Nov 1;22(21):2688-90
pubmed: 16928733
Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
pubmed: 11917018
Curr Biol. 2018 Mar 5;28(5):733-745.e2
pubmed: 29456145
Mol Phylogenet Evol. 2018 May;122:110-115
pubmed: 29421312
Front Plant Sci. 2020 Jun 26;11:829
pubmed: 32670318
New Phytol. 2018 Jan;217(2):855-870
pubmed: 28944472
Genome Res. 2014 Mar;24(3):475-86
pubmed: 24310000
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
BMC Bioinformatics. 2008 Jul 28;9:322
pubmed: 18662388
G3 (Bethesda). 2017 Oct 5;7(10):3349-3357
pubmed: 28866640
Bioinformatics. 2005 Mar 1;21(5):676-9
pubmed: 15509596
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W7-13
pubmed: 20435676
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Mol Biol Evol. 2009 Jul;26(7):1641-50
pubmed: 19377059
PhytoKeys. 2016 Jan 27;(59):1-828
pubmed: 26929706
Nucleic Acids Res. 2005 Jan 20;33(2):511-8
pubmed: 15661851
Sci Adv. 2021 Jun 30;7(27):
pubmed: 34193417
New Phytol. 2016 Jul;211(1):300-18
pubmed: 26900928
Mol Phylogenet Evol. 2021 Aug;161:107171
pubmed: 33798674