Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization

Abstract

Acquisition of mitochondria by the ancestor of all living eukaryotes represented a crucial milestone in the evolution of the eukaryotic cell. Nevertheless, a number of anaerobic unicellular eukaryotes have secondarily discarded certain mitochondrial features, leading to modified organelles such as hydrogenosomes and mitosomes via degenerative evolution. These mitochondrion-derived organelles have lost many of the typical characteristics of aerobic mitochondria, including certain metabolic pathways, morphological traits, and, in most cases, the organellar genome. So far, the evolutionary pathway leading from aerobic mitochondria to anaerobic degenerate organelles has remained unclear due to the lack of examples representing intermediate stages. The human parasitic stramenopile Blastocystis is a rare example of an anaerobic eukaryote with organelles that have retained some mitochondrial characteristics, including a genome, whereas they lack others, such as cytochromes. Here we report the sequence and comparative analysis of the organellar genome from two different Blastocystis isolates as well as a comparison to other genomes from stramenopile mitochondria. Analysis of the characteristics displayed by the unique Blastocystis organelle genome gives us an insight into the initial evolutionary steps that may have led from mitochondria to hydrogenosomes and mitosomes.

FIG. 1.—

Gene and physical map of the Blastocystis MLO genome. Black blocks represent genes and ORFs that are transcribed clockwise (outside of circle) or counterclockwise (inside of circle). Gray blocks represent tRNA genes. tRNA genes are identified by their linked amino acid (single-letter code). M_f and M_e1/M_e2 are initiator and elongator methionyl tRNAs, respectively. The inner circle shows the size scale. The map was created using GenomeViz 1.1 [Ghai et al. 2004]). Because of overlapping coding regions (see text and supplementary table S2, Supplementary Material online), gaps between adjacent genes are not always present.

FIG. 2.—

ML tree of nad proteins. This tree was obtained using the edited alignment produced by MUSCLE v. 3.6, the CpREV+I+G+F amino acid substitution model, and is based on the concatenated amino acid sequences of the nine NADH dehydrogenase genes present in all of the stramenopiles included (i.e., nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, and nad9; see Materials and Methods) as well as in the 12 taxa used as outgroups. Numbers beside the internal nodes are the ML bootstrap values from 400 resamplings obtained with Phyml and the Bayesian MCMC posterior probability values. Black circles indicate 100% bootstrap support and 1.00 posterior probability values. Support values over 50% are shown adjacent to the corresponding nodes. Values below 50% are represented by a dash (–). The clade containing all the stramenopiles is shaded. Taxonomic classification follows the nomenclature of Adl et al. (2005).