Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions

Abstract

Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32-43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

Keywords: Placozoa; evolution; gene order; mitochondrial genome; phylogeny; small inverted repeat.

Fig. 1

Linearized scaled maps of mitochondrial genomes of 14 placozoan haplotypes. The mitogenomes sequenced in this study are marked with asterisks. tRNA genes are indicated by one letter code for the corresponding amino acids. GC percentages (100-bp window) are indicated by the width of gray area. Abbreviations: SIR, small inverted repeat; TR, tandem repeat; ORF, open reading frame of unknown function.

Fig. 2

Fragmentation patterns of cox1, nad5, and 16S in placozoan mitogenomes. The mitogenomes sequenced in this study are marked with asterisks. Exons above and below the line for each haplotype are transcribed in the left–right and right–left direction, respectively. The general exon structure of the respective genes in placozoans is shown at the top. In cox1, each exon length is shown on the top, and in nad5 and 16S, they are indicated above or below each exon, respectively. Group I and group II introns are indicated by black and white dots, respectively. The exons in 16S are labeled according to Signorovitch et al. (2007).

Fig. 3

Phylogenetic relationships of 14 placozoan haplotypes based on complete mitogenome data. (a) Phylogenetic tree based on maximum-likelihood analyses of the concatenated alignment. Bootstrap support values for the different analyses are shown at each node. Mitogenomes newly sequenced in this study are marked with asterisks. (b) Statistical testing of the two major hypotheses on the relationships of haplotypes.

Fig. 4

Summary of the putative succession of the evolution of placozoan mitogenome traits and gene orders. Inferred trait changes are mapped on the placozoan cladogram (left). Gene orders are shown on the right and rearrangements between neighboring haplotypes are indicated in pink. Mitochondrial genes linked in all known placozoans have been merged into gene sections A–N (orange) (see main text for details). Gene sections with identical gene content but with deviating gene orientations compared with clade I are indicated by an asterisk and highlighted in yellow. Specific blocks in H0, H1, H2, H3, and H17, which are explicitly discussed in the text, are enclosed by black dotted lines. Corresponding amino acids of tRNA genes are given as single letter amino acid codes.