Characterization and phylogenetic analyses of ten complete plastomes of Spiraea species.
Chloroplast genome
Phylogenetic analysis
Rosaceae
Spiraea
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
21 Mar 2023
21 Mar 2023
Historique:
received:
12
10
2022
accepted:
10
03
2023
entrez:
22
3
2023
pubmed:
23
3
2023
medline:
24
3
2023
Statut:
epublish
Résumé
Spiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power. In present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported. Although the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.
Sections du résumé
BACKGROUND
BACKGROUND
Spiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power.
RESULTS
RESULTS
In present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported.
CONCLUSIONS
CONCLUSIONS
Although the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.
Identifiants
pubmed: 36944915
doi: 10.1186/s12864-023-09242-3
pii: 10.1186/s12864-023-09242-3
pmc: PMC10029230
doi:
Substances chimiques
Genetic Markers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
137Subventions
Organisme : National Natural Science Foundation of China
ID : 31860052
Organisme : Scientific Elitists Project of Ordinary Colleges and Universities of Guizhou Province
ID : QJH KY [2019] 061
Organisme : Science and Technology Program of Liupanshui
ID : 52020-2019-05-05
Organisme : Science and Technology Program of Liupanshui
ID : 52020-2021-PT-01
Organisme : Science and Technology Program of Liupanshui
ID : 52020-2022-PT-20
Informations de copyright
© 2023. The Author(s).
Références
BMC Evol Biol. 2004 Aug 23;4:27
pubmed: 15324459
J Ethnopharmacol. 1999 Dec 15;68(1-3):209-17
pubmed: 10624880
Genome Biol. 2016 Jun 23;17(1):134
pubmed: 27339192
Proc Natl Acad Sci U S A. 1987 Aug;84(16):5818-22
pubmed: 16593871
Sci Rep. 2017 Jul 18;7(1):5751
pubmed: 28720853
Sci Rep. 2019 Aug 22;9(1):12250
pubmed: 31439882
Bioinformatics. 2003;19 Suppl 1:i54-62
pubmed: 12855437
Sci Rep. 2021 Jul 19;11(1):14643
pubmed: 34282194
Int J Mol Sci. 2020 May 06;21(9):
pubmed: 32384622
Int J Mol Sci. 2021 Oct 16;22(20):
pubmed: 34681821
Bioinformatics. 1998;14(9):817-8
pubmed: 9918953
Bioinformatics. 2003 Aug 12;19(12):1572-4
pubmed: 12912839
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Bioinformatics. 2006 Nov 1;22(21):2688-90
pubmed: 16928733
Mol Biol Evol. 2006 Nov;23(11):2175-90
pubmed: 16916942
Bioinformatics. 2009 Jun 1;25(11):1451-2
pubmed: 19346325
Biomed Res Int. 2019 Mar 19;2019:5046958
pubmed: 31016191
Genome Biol Evol. 2017 Jan 1;9(1):64-76
pubmed: 28172771
BMC Genomics. 2020 Jun 22;21(1):415
pubmed: 32571207
Front Plant Sci. 2016 Jun 14;7:843
pubmed: 27379132
Genomics. 2020 May;112(3):2349-2360
pubmed: 31945463
New Phytol. 2017 May;214(3):1355-1367
pubmed: 28186635
Mol Biol Evol. 2014 Mar;31(3):645-59
pubmed: 24336877
Int J Mol Sci. 2017 Aug 24;18(9):
pubmed: 28837061
Annu Rev Genet. 1985;19:325-54
pubmed: 3936406
Nucleic Acids Res. 2005 Jan 20;33(2):511-8
pubmed: 15661851
J Agric Food Chem. 2020 Dec 9;68(49):14323-14333
pubmed: 32917087
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313
Curr Opin Genet Dev. 1998 Dec;8(6):655-61
pubmed: 9914199
Antioxidants (Basel). 2020 Feb 26;9(3):
pubmed: 32111036