A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes

Abstract

Background: Despite only limited sampling, the holoparasitic plant family Balanophoraceae harbors extreme mito-genome diversity and also has exceptionally divergent plastomes. We therefore sequenced the mitochondrial, plastid, and nuclear genomes of Balanophora yakushimensis and its transcriptome.

Results: At 1.1 Mb, the B. yakushimensis mitogenome is one of the largest known mitogenomes. Driving this expansion and generating the most repeat-rich mitogenome in land plants are many large (up to 200 kb) duplications and a massive proliferation of short, AT-rich repeated sequences. The repeat proliferation, in conjunction with a highly elevated and unusually AT-biased mutation rate, has produced what is by far the most AT-rich land-plant mito-genome. These invasive repeats also created giant introns, unprecedented in size for organelles, and greatly expanded all rDNA exons. We discovered a record-low, for all genomes, transition/transversion ratio (0.12) in B. yakushimensis mtDNA and documented a 26-fold range in this ratio across angiosperm mitogenomes. The B. yakushimensis nuclear genome has lost exceptionally many genes that function in organellar DNA recombination, repair, and replication (RRR). We discuss ways in which these losses-and other genetic alterations as well as non-genetic ones-may or may not be related to the unusual features of both its mitochondrial and plastid genomes.

Conclusions: The mitogenome of B. yakushimensis possesses many exceptional, indeed record-setting properties. The unprecedented loss of nuclear genes for organellar DNA RRR may explain some of these unusual features. These findings expand the boundaries of mitogenome deviancy and raise outstanding questions about the forces driving such extravagantly diversifying evolution.

Keywords: AT-biased base composition; Mitochondrial genomes; Mutation spectrum; Parasitic plants; Photolyases; Repeated sequences.

Fig. 1

The B. yakushimensis mitogenome. A Links among the 21 regions that comprise the genome. Arrows and lines represent regions and links between regions, respectively. Arrow lengths correspond to five size bins of the regions (0–1 kb, 1–10 kb, 10–50 kb, 50–100 kb, and > 100 kb). Resolution of all pathways in this diagram generates the six-chromosome genome map in Fig. S1. B Annotation and features of the 21 regions (see also Fig. S18). Gene annotation, AT content, and repeats are shown in the inner tracks. Genes in blue and green are transcribed clockwise and counter-clockwise, respectively. Grey boxes represent cis-spliced introns. The colored annotation indicates genes that span two regions of Fig. S1

Fig. 2

Variation in cis-spliced intron size and genome size in vascular plant mitogenomes. Taxa were chosen to represent phylogenetic diversity and extremes of intron and genome size. Vertical lines internal to boxes, median intron size; boxes, interquartile range (25th to 75th percentile)

Fig. 3

GC content of 43 angiosperm mtDNAs. Genic values are for 24 core mitochondrial genes, i.e., genes rarely if ever lost from angiosperm mitogenomes. GC3S, GC content at 3rd position synonymous sites; GC4S, GC content at fourfold synonymous sites. Asterisks mark assemblies that are too incomplete for genome and cis-intron GC content to be estimated. See Table S9 for exact values

Fig. 4

GC content, repeat content, and gene annotation in regions C and M of the B. yakushimensis mitogenome. See Fig. S18 for analysis of all 21 regions

Fig. 5

Variation in mutation spectra. A Ti/Tv variation in Balanophoraceae mitochondrial protein genes. Santalales portion of the topologically constrained, synonymous site tree of Fig. S29, with the six internal Balanophoraceae branches numbered. Ti/Tv values are in parentheses. B Mutation spectra for Balanophoraceae branches (Table S12) and the six other mtDNA branches with significant transversion biases (Table S15). These six include five Piperales branches [P/H, the branch leading to Hydnora (Hyd) and Prosopanche (Pro); and T/A, the branch leading to Thottea (Tho) and Aristolochia] and the Carica branch (Car). Ti/Tv values of the eight branches with significant transversion biases are in blue

Fig. 6

Root-to-tip synonymous-site (ds) branch lengths of 32 mitochondrial protein genes from 98 diverse angiosperms. Vertical lines, median values; boxes, interquartile range (25th to 75th percentile); black dots, outliers exclusive of many of the colored circles. Red-filled circles mark values for Balanophora. Open circles mark values for taxa with very high ds values for a minority of genes (Ajuga) or a majority (other taxa). The number of genes used for these taxa is in parentheses

Fig. 7

Loss of organelle DNA-RRR genes and features of organelle genome evolution in Balanophoraceae. Colors denote targeting status as per key at top left. *FPG1 is present in B. fungosa and B. subcupularis, which otherwise lack all genes that are missing from B. yakushimensis and have no additional losses (Table S22). Phylogenetic relationships are based on Ceriotti et al. [121] and Kim et al. [123]