Abstract
In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species. The chloroplast genomes of Adoxaceae species ranged in size from 157,074 bp (Sinadoxa corydalifolia) to 158,305 bp (Sambucus williamsii), and the plastid genomes of Caprifoliaceae varied from 154,732 bp (Lonicera fragrantissima var. lancifolia) to 156,874 bp (Weigela florida). The differences in the number of genes in Caprifoliaceae and Adoxaceae species were largely due to the expansion and contraction of inverted repeat regions. In addition, we found that the number of dispersed repeats (Adoxaceae = 37; Caprifoliaceae = 384) was much higher than that of tandem repeats (Adoxaceae = 34; Caprifoliaceae = 291) in Dipsacales species. Interestingly, we determined 19 genes with positive selection sites, including three genes encoding ATP protein subunits (atpA, atpB, and atpI), four genes for ribosome protein small subunits (rps3, rps7, rps14, and rps15), four genes for photosystem protein subunits (psaA, psaJ, psbC, and pabK), two genes for ribosome protein large subunits (rpl22 and rpl32), and the clpP, infA, matK, rbcL, ycf1, and ycf2 genes. These gene regions may have played key roles in the adaptation of Dipsacales to diverse environments. In addition, phylogenetic analysis based on the plastid genomes strongly supported the division of 14 Dipsacales species into two previously recognized sections. The diversification of Adoxaceae and Caprifoliaceae was dated to the late Cretaceous and Tertiary periods. The availability of these chloroplast genomes provides useful genetic information for studying taxonomy, phylogeny, and species evolution in Dipsacales.
Highlights
The order Dipsacales comprises the families Valerianaceae, Dipsacaceae, Adoxaceae, and Caprifoliaceae sensu lato (Cronquist, 1979; Thorne, 1992)
The cp genomes of the six Adoxaceae species ranged in size from 157,074 bp (S. corydalifolia) to 158,305 bp (S. williamsii), and the eight Caprifoliaceae cp genomes ranged from 154,732 bp (L. fragrantissima var. lancifolia) to 156,874 bp (W. florida) (Figure 1 and Table 1)
The LSC length in the six Adoxaceae cp genomes ranged from 86,171 bp (S. corydalifolia) to 86,810 bp (S. williamsii), and the SSC and inverted repeats (IRs) lengths ranged from 18,338 bp (V. betulifolium) to 18,993 bp (S. williamsii) and 26,112 bp (A. moschatellina) to 26,462 bp (V. betulifolium), respectively
Summary
The order Dipsacales comprises the families Valerianaceae, Dipsacaceae, Adoxaceae, and Caprifoliaceae sensu lato (including Linnaeaceae, Diervillaceae, and Caprifoliaceae sensu stricto) (Cronquist, 1979; Thorne, 1992). The general consensus is that Dipsacales comprises a monophyletic taxon with two major lineages (Donoghue et al, 1992; Olmstead et al, 1993, 2000; Zhang et al, 2003): (i) the large clade Caprifoliaceae containing Diervilleae, Caprifolieae, Linnaeeae, Morinaceae, Valerianaceae, and Dipsacaceae; and (ii) the smaller clade comprising the family Adoxaceae, which contains the genera Viburnum, and Sambucus, Sinadoxa, Tetradoa, and Adoxa. Other studies based on cp DNA regions trnL-trnF and ndhF, as well as mitochondrial DNA sequence variations have suggested that the genera Dipelta and Kolkwitzia have a very close evolutionary relationship (Donoghue et al, 2001; Zhang et al, 2002; Winkworth et al, 2008). These previous studies have resolved the basic phylogenetic relationships among Dipsacales, but the interspecific divergence and lineage structure of some main genera (e.g., Dipelta, Kolkwitzia, and Weigela) still remain largely controversial
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