High variability of mitochondrial gene order among fungi

Abstract

From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mt genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.

Keywords: Basidiomycota; basal fungi; endosymbiosis; fungal phylogeny; genome size reduction; rearrangement rates; sordariomycetes.

Fig. 1.—

ML phylogeny of our sampled taxa including the 38 species in the dikarya data set. The gene tree was inferred from a concatenated alignment of 14 single-copy orthologous genes (atp6, atp8, atp9, nad1–nad6, nad4L, cob, and cox1–cox3). RAxML v.7.2.6 (Stamatakis 2006) was used assuming the LG substitution matrix and default parameters. On the right side of each taxon name is a series of colored boxes representing the mt gene order according to GenBank annotation. Bootstrap support appears next to each node. bsGOL values are shown next to each species name, and they are estimated by minimizing the following expression: L = ∑(∑b_i,jx_j – GOL_i)², where b_i,j is a Boolean variable that specifies the branches that are relevant for the estimation of a particular bsGOL (i.e., 0 if it is not relevant and 1 if it is), x_j is obtained by minimizing L and is the actual bsGOL value, and GOL_i are the estimatedvalues from the pairwise comparisons, in other words, GOL_i = 1 − GOC_i (see Fischer et al. 2006 for more details). Significant tRNA clustering was found in species marked with a spiral. This figure was made using the ETE python environment for tree exploration (Huerta-Cepas et al. 2010).

Fig. 2.—

GOC between pairs of genomes of the dikarya data set as a function of their phylogenetic (patristic) distance. Distances were estimated using the estimated branch lengths in figure 3, listed in table 2. Models are fitted by nonlinear regression. Model 0: GOC = 2/1+e^αt. Model 1: GOC = 1 – √αt. Model 2: 1/GOC = αt + 1. Model 3: GOC = p^t, where parameter α is adjusted by regression and t is the patristic distance between the two compared taxa.

Fig. 3.—

Pearson’s correlation between bsGOC values and branch lengths (R = 0.7, P value < 0.0005) for the dikarya data set.

Fig. 4.—

Pairwise GOC values as a function of the phylogenetic (patristic) distance between them, for the dikarya data set. Here, we conducted a randomization test as follows: for each genome, we listed the order of genes, made all possible pairwise comparisons of these lists, estimated the GOC score (Rocha 2006), shuffled randomly the gene order, and estimated a new GOC value. We obtained 100,000 reshufflings and compared the original GOC to the distribution of the shuffled GOCs. We applied the Bonferroni correction for multiple testing and determined the significance (P values) of the comparisons. The red dots represent significant P values, which correspond to the group of sordariomycetes (in fig. 1, the clade grouping Chaetomium thermophilum, Podospora anserina, Gibberella zeae, F. oxysporum, Lecanicillium muscarium, Cordyceps bassiana, Beauveria bassiana, and Metarhizium anisopliae).