The First Plastid Genome of the Holoparasitic Genus Prosopanche (Hydnoraceae)

Abstract

Plastomes of parasitic and mycoheterotrophic plants show different degrees of reduction depending on the plants' level of heterotrophy and host dependence in comparison to photoautotrophic sister species, and the amount of time since heterotrophic dependence was established. In all but the most recent heterotrophic lineages, this reduction involves substantial decrease in genome size and gene content and sometimes alterations of genome structure. Here, we present the first plastid genome of the holoparasitic genus Prosopanche, which shows clear signs of functionality. The plastome of Prosopanche americana has a length of 28,191 bp and contains only 24 unique genes, i.e., 14 ribosomal protein genes, four ribosomal RNA genes, five genes coding for tRNAs and three genes with other or unknown function (accD, ycf1, ycf2). The inverted repeat has been lost. Despite the split of Prosopanche and Hydnora about 54 MYA ago, the level of genome reduction is strikingly congruent between the two holoparasites although highly dissimilar nucleotide sequences are observed. Our results lead to two possible evolutionary scenarios that will be tested in the future with a larger sampling: 1) a Hydnoraceae plastome, similar to those of Hydnora and Prosopanche today, existed already in the most recent common ancestor and has not changed much with respect to gene content and structure, or 2) the genome similarities we observe today are the result of two independent evolutionary trajectories leading to almost the same endpoint. The first hypothesis would be most parsimonious whereas the second would point to taxon dependent essential gene sets for plants released from photosynthetic constraints.

Keywords: Hydnora; Hydnoraceae; Piperales; Prosopanche; holoparasite; parasitic plants; plastid genome.

Figure A1

Dotplot comparison of the plastomes of Prosopanche americana and Hydnora visseri (NC_029358) highlights differences on nucleotide level and inversion (red circle). The diagonal lines indicate sequence similarity between the plastomes of Hydnora and Prosopanche, the gaps visualize areas of drastic nucleotide sequence differences. The red circle highlights the larger of the two inversions between the Hydnoraceae plastomes. The dotplot was created with Geneious (v 11.1.5) by using an exact score matrix, a window size of 100 and a threshold of 200.

Figure 1

The plastid genome of Prosopanche americana is found on a single scaffold. a) Stoichiometry plot of the scaffold lengths and the respective mean coverage depth of the Prosopanche americana assembly. Scaffolds are visualized as blue circles. The green dots represent scaffolds with BLAST hits for annotated fractions of the plastome (derived from “gene features” in NCBI). The black arrow points to scaffold 424. b) Distribution of the reads mapped to the linear scaffold 424 with the scale displaying the depth of coverage in 1k increments. The red boxes represent the coverage of the Prosopanche amercana repeat regions.

Figure 2

The highly reduced plastome of Prosopanche americana. The circular plastome of holoparasitic Prosopanche americana contains 24 unique genes (14 ribosomal protein genes, 4 ribosomal RNA genes, five genes coding for transfer RNAs and three genes with other or unknown function), which are distributed over a total length of 28,191 bp. Gene distribution is displayed on the outer circle with color coded gene groups according to the legend (bottom left). GC content is visualized as inner, grey circle. * indicates genes with introns.

Figure 3

Prosopanche americana trnI-CAU repeat region. Alignment of the two trnI-CAU repeat copies highlights high sequence identity (green identity bar) over 195 bp with only four nucleotide differences (arrows pointing to gaps in identity graph and nucleotide differences highlighted by color and nucleotide code in sequence alignment). The trnI-CAU gene is fully contained within the repeat whereas only 25 bp of the rpl2 gene start fall within repeat borders. Contrary to copy B, which stays with a truncated rpl2 pseudogene, copy A is preceded by the complete rpl2 ORF of Prosopanche americana.

Figure 4

Prosopanche americana has a low GC content. (a) Comparison of the GC content and (b) proportional changes of plastid genome compartments (protein coding, ribosomal RNA, intergenic region) among the photosynthetic Aristolochia contorta (Aristolochiaceae, NC_036152) and the holoparasitic Hydnoraceae highlighting the extent of changes the plastomes of the Hydnoraceae have undergone with respect to nucleotide composition and conservation of specific genome regions.

Figure 5

High structural similarity between the plastomes of Hydnoraceae. Linear plastid genome comparison of Prosopanche americana and Hydnora visseri (NC_029358). Genes are color coded; the dotted lines highlight inversions between the two genomes compared, genes containing introns are marked with *.

Figure 6

High mutational rate within Hydnoraceae relative to other Piperales and diverse photosynthetic angiosperms. Phylogenetic maximum likelihood tree reconstruction as cladogram (left) and phylogram (right) estimated using RAxML with the GTR + I + G model and conducting rapid bootstrapping (1000 replicates) recovers Hydnora and Prosopanche as sister genera and Hydnoraceae together as sister to a sister group of Aristolochioideae and Asaroideae (both Aristolochiaceae) within the Piperales. Bootstrap support values are displayed above the nodes. The scale bar shows the number of substitutions per site. Ingroup taxa are color coded, with eudicots being green, monocots red, Piperales dark blue and remaining Magnoliids and ANITA grade taxa light blue. Taxa refer to the dataset of Jansen et al. [42] if not otherwise indicated by GenBank number.