Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals

Abstract

Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.

Fig 1. Eternal morphology of kinorhynchs.

A. Pycnophyes kielensis, scale bar = 500 μm; B. Echinoderes svetlanae, scale bar = 200 μm. Heads orient down.

Fig 2. Predicted mitochondrial methionine tRNAs of Echinoderes svetlanae and Pycnophyes kielensis.

Compensatory changes are shown in red. Compensatory change in M1 –the first pair of the anticodon stem (U-A in E. svetlanae and C-G in P. kielensis). Compensatory changes in M2 –the first pair of the T-arm (U-A in E. svetlanae and C-G in P. kielensis) and the fifth pair of the anticodon stem (G-C in E. svetlanae and A-U in P. kielensis).

Fig 3. Bayesian tree based on the alignment of tRNA genes from E. svetlanae and P. kielensis.

Numbers at the branches indicate Bayesian posterior probabilities. Methionine tRNA genes are marked orange. tRNA specificity is coded by one letter.

Fig 4. Bayesian tree based on the concatenated dataset of 13 protein-coding genes from mitochondrial genomes after removing constant positions and fast-evolving sites from the alignment.

Numbers at the branches indicate Bayesian posterior probabilities as percent values.

Fig 5. Protein-coding and rRNA gene orders in the mitochondrial genomes of E. svetlanae and P. kielensis.

Fig 6. Kinorhynch gene orders and conservative blocks of mitochondrial genes from Bilateria.

Genes and blocks are colored and named following [14].

Fig 7. Gene orders of E. svetlanae, Priapulida and Panarthropoda [15] with Deuterostomia [17] as an outgroup.

Fig 8. Putative model of gene order evolution in Protostomia reconstructed by TreeREx.

Genes are colored following [14].