Characterization and phylogenetic analyses of ten complete plastomes of Spiraea species

Abstract

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: 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: 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.

Keywords: Chloroplast genome; Phylogenetic analysis; Rosaceae; Spiraea.

Fig. 1

Chloroplast genome map of Spiraea. The grey inside circle indicates the GC level of every genomic position. Genes inside in the outer circle of genomic map are transcribed clockwise and vice versa. The different functional gene categories are shown in the different colors

Fig. 2

SSR loci analysis of fifteen Spiraea. (A) Number of six SSRs types; (B) Number of SSRs in LSC, SSC, and IR regions, respectively

Fig. 3

Colinear analysis of fifteen Spiraea species chloroplast genomes. The collinear blocks are marked with the same color

Fig. 4

The $\pi$ values of the fifteen Spiraea chloroplast genome sequences by sliding window analysis (window length: 600 bp with step size of 200 bp)

Fig. 5

Phylogenetic tree of the fifteen Spiraea species inferred by maximum likelihood (ML) and Bayesian inference (BI) methods based on the complete plastomes. Numbers at nodes correspond to ML bootstrap percentages and BI posterior probabilities

Fig. 6

Phylogenetic tree of the fifteen Spiraea species inferred by maximum likelihood (ML) and Bayesian inference (BI) methods based on the combined six mutational hotspot regions. Numbers at nodes correspond to ML bootstrap percentages and BI posterior probabilities