| Mitochondria, found in nearly all eukaryotes, are indispensable double membrane organelles that play pivotal roles in several cellular processes. While diversity of mitochondrial genomes among eukaryotes has been recognized, it was thought that animal mitochondrial genomes are small circular molecules with little variation in size and gene content. However this picturing of animal mitochondrial genomes was based on a biased sampling drawn primarily from bilaterian animals. In order to explore the diversity and understand the evolution of mitochondrial genomes in animals, we sequenced and analyzed mitochondrial genomes from all 14 orders of demosponges, the biggest class within sponges (phylum Porifera). Comparative genome analysis shows that a large variation in mitochondrial genome architecture is present within this group exceeding that found within Bilateria. Phylogenomic analyses based on mtDNA data support demosponges as a monophyletic group and suggest that the last common ancestor of animals might have had a tissue-level organization. Although transfer RNA (tRNA) genes are generally conserved in these genomes, evidences were found for horizontal evolution of some tRNA genes that cautioned the use of tRNA phylogeny to infer genetic code evolution. While animal mitochondrial genomes only encode a handful of proteins, the complex functions of mitochondria require over a thousand of proteins that more than 98% are nuclear encoded. Comparative gene family analyses for nuclear encoded mitochondrial proteins demonstrate that protein subcellular relocalization enabled the retention and gain of function of genes after duplications and provided a way for recruiting mitochondrial proteins. In addition, mitochondrial proteome also expanded through subfunctionalization mechanism after gene duplications. |
