Novel perspectives on plastome evolution in Onagraceae

Abstract

Previous systematic studies have generated abundant information on plants in family Onagraceae Juss., making this taxonomic group a model for understanding plant evolution. The chloroplast genome is widely used to provide valuable insights into how plant lineages evolved. In the present study, we employed shotgun sequencing to assemble new plastomes from Onagraceae. Plastomes of ten species and one genus, Fuchsia, are reported for the first time. We characterize and compare the plastome features of six genera (Chamaenerion, Circaea, Epilobium, Fuchsia, Ludwigia, and Oenothera), allowing us to reconstruct their phylogenies and explore inter- and infra-generic evolutionary relationships, inverted repeat (IR) expansion, plastome size increases, and correlations among repeat elements, genetic variations, and evolutionary events. Our findings indicate that each of the tribes and subfamilies we assessed exhibits unique plastome features. Our phylogenetic tree supports previous findings, but also reveals that some clades need further systematic analyses. We show that increased plastome size within subfamily Onagroideae coincides with IR expansion, which is not the case for subfamily Ludwigioideae. In addition, our results indicate that higher repeat numbers and greater genetic variation can serve as indicators of evolutionary events, such as gene loss and gain, IR boundary shifts, and inversions, but they may not have arisen universally across all members of Onagraceae. Our study provides some novel insights into plastome evolution in the Onagraceae. Further studies should aim to elucidate how plastome size has evolved in Ludwigioideae and explore the evolutionary roles of regions in Onagraceae plastomes exhibiting high repeat numbers and genetic variations.

Figure 1.

Summary of the complete chloroplast genome of Onagraceae (155,111 bp – 167,092 bp) using Fuchsia lycioides as a basis. The four rings from outside to inside show the locations of genes, microsatellites, tandem repeats, and forward (red) and reverse (green) repeats, respectively. Genes are color-coded according to their function, as per the legend. Genes inside the first ring are in clockwise directions, whereas genes on the outside are in counterclockwise directions. Large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions are annotated on the second ring.

Figure 2.

Bayesian 50% majority rule consensus tree based on 33 Onagraceae and three Lythraceae plastomes. The arrow indicates the crown node of Onagraceae. Ch, Ci, E, F, L, and O denote the crown nodes of Chamaenerion, Circaea, Epilobium, Fuchsia, Ludwigia, and Oenothera, respectively. In cases where branches are not fully supported, posterior probabilities (pp)/bootstrapping (bs) values are shown. Hyphens indicate if the pp or bs value is less than 0.70 or 50, respectively. Bars on the tree indicate gene or intron loss and regain events. Vertical lines at the right of the tree indicate the two Onagraceae subfamilies and tribes of Onagroideae. Branch lengths are shown in (a) and Supporting Information File S2, and have been transformed in (b). The scale bar denotes the branch length.

Figure 3.

Comparisons of the boundaries of the large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions of plastomes in the six genera of the Onagraceae in this analysis indicate that each genus displays a unique pattern with a few variations. The phylogenetic tree in the left panel refers to Fig. 2, and the arrow indicates the crown node of the Onagraceae. Thick black lines represent the plastome sequences. Genes near the boundaries are shown on the plastome sequences as colored solid boxes, whereas pseudogenes are shown as colored open boxes or ψ. Thin arrows with numbers denote the lengths between region boundaries and the start or end of genes/pseudogenes.

Figure 4.

Nucleotide variations (Pi; π) for plastomes within (a) Oenothera, (b) Epilobium, (c) Chamaenerion, (d) Circaea, (e) subfamily Onagroideae, (f) Ludwigia or subfamily Ludwigioideae, and (g) family Onagraceae based on the a priori alignment with the modified plastome (mpAL), in which the 56-kb inversion of Oenothera biennis has been inverted. The complete chloroplast genome of Fuchsia lycioides (h) is shown here as a reference to indicate the positions and directions of genes on the mpAL, with genes color-coded as in Fig. 1. Eleven regions with high π are annotated with letters. Genes, spacers, quadripartite structure boundaries, and evolutionary events found in these regions are listed in Table 4.

Figure 5.

(a) Average pairwise sequence identities (APSI) and (b) average repeat numbers for each chloroplast gene and spacer in Onagraceae. Genes or spacers with lower APSI are denoted with letters. The positions of each gene and spacer on the complete chloroplast genome (relative to the Fuchsia lycioides plastome shown at the bottom) are shown along the x-axis. Note that only one reverted repeat is displayed in (a) and (b). Regions with low APSI or high average repeat numbers are annotated with letters. Genes, spacers, quadripartite structure boundaries, and evolutionary events found in these regions are listed in Table 4.