Heartwater, a tick-borne disease of domestic and wild ruminants, is caused by the intracellular rickettsia Ehrlichia ruminantium (previously known as Cowdria ruminantium). It is a major constraint to livestock production throughout subSaharan Africa, and it threatens to invade the Americas, yet there is no immediate prospect of an effective vaccine. A shotgun genome sequencing project was undertaken in the expectation that access to the complete protein coding repertoire of the organism will facilitate the search for vaccine candidate genes. We report here the complete 1,516,355-bp sequence of the type strain, the stock derived from the South African Welgevonden isolate. Only 62% of the genome is predicted to be coding sequence, encoding 888 proteins and 41 stable RNA species. The most striking feature is the large number of tandemly repeated and duplicated sequences, some of continuously variable copy number, which contributes to the low proportion of coding sequence. These repeats have mediated numerous translocation and inversion events that have resulted in the duplication and truncation of some genes and have also given rise to new genes. There are 32 predicted pseudogenes, most of which are truncated fragments of genes associated with repeats. Rather then being the result of the reductive evolution seen in other intracellular bacteria, these pseudogenes appear to be the product of ongoing sequence duplication events.gene duplication ͉ bacterial genome ͉ molecular sequence data ͉ intracellular adaptation E hrlichia ruminantium (previously known as Cowdria ruminantium) is an obligate intracellular bacterium in the order Rickettsiales. Species in this order cause serious diseases in man and domestic animals throughout the world. E. ruminantium is transmitted by ticks of the genus Amblyomma and causes heartwater, a fatal and economically important disease of wild and domestic ruminants. The disease occurs throughout subSaharan Africa and on several Caribbean islands, from which it threatens to invade the Americas (1), but the existing immunization procedures are rudimentary and relatively ineffective (2). E. ruminantium is a fragile bacterium with exacting culture requirements in eukaryotic cell lines; genetic manipulation has not been attempted, and little is known about its mechanisms of virulence or pathogenesis. Heartwater affects all domestic ruminants, and 80-95% of naïve animals die within 3 weeks, but those that recover have a T cell-mediated immunity to subsequent homologous challenge (3). In the absence of any directed strategy to identify T cell-stimulatory proteins we sequenced the E. ruminantium genome in the expectation that access to the complete protein-coding repertoire of the organism would facilitate the search for vaccine candidate genes.

We sequenced 18S rRNA genes of a calcareous sponge, Clathrina cerebrum, a demosponge, Axinella polypoides, and a zoanthid cnidarian, Parazoanthus axinellae. Our phylogenetic analysis supports the monophyly of kingdom Animalia and confirms that choanoflagellate protozoans are their closest relatives. Sponges as a whole are monophyletic, but possibly paraphyletic; demosponges and hexactinellids form a monophyletic group of silicious sponges. Our phylogenetic trees support a monophyletic origin of the nervous system in the immediate common ancestor of Cnidaria and Ctenophora. They weakly suggest that animals with a nervous system may be more closely related to calcareous sponges than to silicious sponges; the nervous system might have originated in an early calcareous sponge. Our trees confirm that Myxozoa and Placozoa are animals that arose by secondary loss of the nervous system, but suggest that Myxozoa may be sisters of, rather than derived from, Bilateria. Kingdom Animalia is divided into four subkingdoms: Radiata (Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa, and Bilateria. The 18S rRNA genes of Myxozoa evolved over twice as fast as in Radiata. Comparison with the fossil record reveals a brief 10-fold (or greater) acceleration in the rate of rRNA evolution in early Bilateria followed by normal low rates for about 500 million years.