Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses.
Choloplast genome
Molecular marker
Phylogenetic relationships
Sium
Species identification
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
25 Jul 2023
25 Jul 2023
Historique:
received:
22
10
2022
accepted:
12
07
2023
medline:
27
7
2023
pubmed:
25
7
2023
entrez:
24
7
2023
Statut:
epublish
Résumé
Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.
Sections du résumé
BACKGROUND
BACKGROUND
Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.
RESULTS
RESULTS
The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.
CONCLUSIONS
CONCLUSIONS
The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.
Identifiants
pubmed: 37488499
doi: 10.1186/s12870-023-04376-8
pii: 10.1186/s12870-023-04376-8
pmc: PMC10367252
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
368Subventions
Organisme : National Natural Science Foundation of China
ID : 31960048
Organisme : Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province
ID : YNWRQNBJ-2019-208
Organisme : department of Science and Technology of Yunnan Province
ID : 202201AT070118
Organisme : Hundred Talents Program of Kunming Medical University
ID : 60118260127
Organisme : Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province
ID : 202205AM070006
Informations de copyright
© 2023. The Author(s).
Références
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W575-81
pubmed: 23609545
Am J Bot. 2006 Dec;93(12):1828-47
pubmed: 21642128
Am J Bot. 2017 Feb;104(2):296-312
pubmed: 28202452
Nucleic Acids Res. 2019 Jul 2;47(W1):W65-W73
pubmed: 31066451
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Am J Bot. 2006 May;93(5):747-61
pubmed: 21642138
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Genes (Basel). 2017 Apr 19;8(4):
pubmed: 28422071
Am J Bot. 2007 Mar;94(3):275-88
pubmed: 21636401
Brief Bioinform. 2008 Jul;9(4):286-98
pubmed: 18372315
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Genet Res Int. 2015;2015:431487
pubmed: 25874132
Mol Phylogenet Evol. 2017 Mar;108:1-21
pubmed: 28179182
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
pubmed: 15215394
PeerJ. 2019 Nov 21;7:e8063
pubmed: 31772837
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
BMC Plant Biol. 2019 Jul 2;19(1):290
pubmed: 31266465
Am J Bot. 2014 Nov;101(11):1987-2004
pubmed: 25366863
BMC Plant Biol. 2021 Jan 7;21(1):26
pubmed: 33413122
BMC Plant Biol. 2023 May 29;23(1):284
pubmed: 37246219
Am J Bot. 2005 Jan;92(1):142-66
pubmed: 21652394
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Biol Evol. 2009 Jan;26(1):99-110
pubmed: 18922764
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
BMC Plant Biol. 2012 May 01;12:61
pubmed: 22548759
Mol Phylogenet Evol. 2008 Mar;46(3):1129-50
pubmed: 18178486
Bioinformatics. 2017 Aug 15;33(16):2583-2585
pubmed: 28398459
Mob Genet Elements. 2012 Nov 1;2(6):261-266
pubmed: 23481035
Bioinformatics. 2018 Sep 1;34(17):3030-3031
pubmed: 29659705
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Mol Phylogenet Evol. 2021 Aug;161:107183
pubmed: 33892097
BMC Genomics. 2006 Aug 31;7:222
pubmed: 16945140
Mol Phylogenet Evol. 2009 Oct;53(1):56-68
pubmed: 19501179
BMC Plant Biol. 2020 May 28;20(1):242
pubmed: 32466748
Front Plant Sci. 2019 Apr 09;10:429
pubmed: 31024595
Ecol Evol. 2018 Dec 26;9(1):364-377
pubmed: 30680120