Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family

Abstract

Nonphotosynthetic plants possess strongly reconfigured plastomes attributable to convergent losses of photosynthesis and housekeeping genes, making them excellent systems for studying genome evolution under relaxed selective pressures. We report the complete plastomes of 10 photosynthetic and nonphotosynthetic parasites plus their nonparasitic sister from the broomrape family (Orobanchaceae). By reconstructing the history of gene losses and genome reconfigurations, we find that the establishment of obligate parasitism triggers the relaxation of selective constraints. Partly because of independent losses of one inverted repeat region, Orobanchaceae plastomes vary 3.5-fold in size, with 45 kb in American squawroot (Conopholis americana) representing the smallest plastome reported from land plants. Of the 42 to 74 retained unique genes, only 16 protein genes, 15 tRNAs, and four rRNAs are commonly found. Several holoparasites retain ATP synthase genes with intact open reading frames, suggesting a prolonged function in these plants. The loss of photosynthesis alters the chromosomal architecture in that recombinogenic factors accumulate, fostering large-scale chromosomal rearrangements as functional reduction proceeds. The retention of DNA fragments is strongly influenced by both their proximity to genes under selection and the co-occurrence with those in operons, indicating complex constraints beyond gene function that determine the evolutionary survival time of plastid regions in nonphotosynthetic plants.

Figure 1.

Physical Maps of the Plastid Chromosomes of Photosynthetic and Nonphotosynthetic Members of Orobanchaceae. All genes are colored according to functional complexes. Pseudogenes are indicated by Ψ. Brackets on top indicate different lifestyles.

Figure 2.

Repeat DNA in Plastomes of Orobanchaceae. (A) Proportions of different repeat types in plastomes of 11 Orobanchaceae species and tobacco. Numbers above individual repeat columns indicate the repeat density, where, for example, 1/500 means that one repeat occurs every 500 bp. The direction is given for each repeat type. (B) Evolution of repeats in Orobanchaceae. The strong evolutionary trend of increasing numbers of repetitive DNA in plastid genomes after the transition to heterotrophy is shown by the P value from an LRT evaluating constant-variance random walk versus directional random walk models to explain repeat variation. The number of repeats is illustrated by differently sized triangles at the tip of each terminal branch. Brackets indicate different lifestyles.

Figure 3.

Series of Functional and Physical Losses of Plastid Genes. Graphical summary of the number of gene losses (A) and the losses of functional classes of genes (B) based on the reconstruction of plastid gene contents at ancestral nodes in Orobanchaceae. Pseudogenization is illustrated above the branches, whereas gene deletion is shown below the branches. In (A), an arrow indicates the correct placement of a value, and in (B), dots mark loss-of-function deletions (i.e., those without pseudogenization at any of the parent nodes).

Figure 4.

Evolution of Plastomes Based on Likelihood Reconstructions of Ancestral Gene Contents and the Rearrangement History. The reconstructed plastid LSCs plus their adjacent regions are shown at all nodes of the Orobanchaceae phylogeny (thick gray lines), except for the ancestor of Phelipanche and Myzorrhiza because it differs from M. californica only by having not yet lost rpoC1, petN, psaA, petL, and ndhH. Pseudogenes are indicated by gray gene boxes and gene names with a Ψ-prefix, whereas deletions are indicated by black arrowheads and the corresponding gene name(s). Gene labels with an asterisk indicate intron losses. Blue pennons indicate the breakpoints of an inversion (I1 to I5); the range and orientation of these inversions are denoted in both the ancestral and the derived plastid genome, and the genes flanking inversion breakpoints are labeled accordingly. For simplicity, SSC and IR are not shown here.

Figure 5.

Evolution of GC Content in Plastomes of Orobanchaceae. (A) A strong evolutionary trend of reduction in total GC content occurs with the transition from an autotrophic to a parasitic lifestyle and continues in nonphotosynthetic lineages. P values from LRTs at key nodes of lifestyle changes evaluate constant-variance random walk versus directional random walk models to explain GC variation in parasites and nonparasites. (B) GC content at different codon positions of intact plastid protein-coding genes for nine nonphotosynthetic and four photosynthetic plants. (C) Variation of GC content at different codon positions in coding regions of parasites and nonparasites assessed as the difference (ΔGC) to a reference genome (Aucuba japonica, Garryaceae). In (B) and (C), a line inside each box designates the median across 31 conserved plastid genes; the whisker ends are at the 5th and 95th percentiles.