DOI: 10.5061/dryad.v15dv41sm
title: An animal without a mitochondrial genome: the salmon parasite Henneguya salminicola (Cnidaria: Myxozoa)

description: Although aerobic respiration is a hallmark of eukaryotes, a few
 unicellular lineages, growing in hypoxic environments, have secondarily
 lost this ability. In the absence of oxygen, the mitochondria of these
 organisms have lost all or parts of their genomes and evolved into
 mitochondria related organelles (MROs). There has been debate regarding
 the presence of MROs in animals. Using deep sequencing approaches, we
 discovered that a member of the Cnidaria, the myxozoan Henneguya
 salminicola, has no mitochondrial genome, and thus has lost the ability to
 perform aerobic cellular respiration. This is the only animal described
 without these core eukaryotic features. Our analyses suggest that H.
 salminicola lost not only its mitochondrial genome, but also nearly all
 nuclear genes involved in transcription and replication of the
 mitochondrial genome. In contrast, we identified many genes that encode
 proteins involved in other mitochondrial pathways and determined that
 genes involved in aerobic respiration or mitochondrial DNA replication
 were either absent, or present only as pseudogenes. As a control, we used
 the same sequencing and annotation methods to show that the
 closely-related myxozoan, Myxobolus squamalis, has a mitochondrial genome.
 The molecular results are supported by fluorescence micrographs, which
 show the presence of mitochondrial DNA in M. squamalis but not in H.
 salminicola. Our discovery confirms that adaptation to an anaerobic
 environment is not unique to single-celled eukaryotes but has also evolved
 in a multicellular, parasitic animal. Hence, H. salminicola provides
 an opportunity for understanding the evolutionary transition from
 an aerobic to an exclusive anaerobic metabolism.
description: Two matrices were selected from a database of 78
 ribosomal protein coding genes, which has been curated manually to avoid
 contamination and structural annotation errors. The first dataset included
 78 species representative of major eukaryote lineages; the second included
 129 species that encompassed animal diversity and their closest outgroup
 (choanoflagellates, ichthyosporean and ministeriid). In both datasets,
 sequences were concatenated with SCaFoS. After removal of any ambiguously
 aligned positions using Gblocks Version 0.91b, with default parameter
 values, these Eukaryote and Metazoa datasets included 9,490 and 11,352
 amino acid positions, respectively. Phylogenetic reconstructions were
 performed using the site-heterogeneous CAT model, which reduces the impact
 of long branch attraction, as implemented in Phylobayes MPI vs.1.5. For
 both datasets, two independent chains were run for 10,000 cycles. The
 first 5,000 trees from each chain were discarded as burn-in. Chain
 convergence was assessed using the bpcomp and tracecomp scripts which are
 part of Phylobayes. Specifically, for both analyses the bpcomp maxdiff
 values were &lt;0.3 and the tracecomp effsize values were &gt;70
 (except for eukaryotes where the tree length value was 21), indicating a
 proper convergence.
description: The trees are in Newick format. The matrices
 are in Nexus format, the different gene partitions are indicated in the
 "Set Block" (under the matrix).