A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp.  of domestic fowl and associated with multiple developmental stages. 
Coccidiosis of the domestic fowl is a worldwide disease caused by seven species of protozoan parasites of the genus Eimeria.  The genome of the model species, Eimeria tenella, presents a complexity of 55-60MB distributed in 14 chromosomes.  Relatively few studies have been undertaken to unravel the complexity of the transcriptome of Eimeria parasites.  We report here the generation of more than 45,000 open reading frame expressed sequence tag (ORESTES) cDNA reads of E. tenella, Eimeria maxima and Eimeria acervulina, covering several developmental stages: unsporulated oocysts, sporoblastic oocysts, sporulated oocysts, sporozoites and second generation merozoites.  All reads were assembled to constitute gene indices and submitted to a comprehensive functional annotation pipeline.  In the case of E. tenella, we also incorporated publicly available ESTs to generate an integrated body of information.  Orthology analyses have identified genes conserved across different apicomplexan parasites, as well as genes restricted to the genus Eimeria.  Digital expression profiles obtained from ORESTES/EST countings, submitted to clustering analyses, revealed a high conservation pattern across the three Eimeria spp.  Distance trees showed that unsporulated and sporoblastic oocysts constitute a distinct clade in all species, with sporulated oocysts forming a more external branch.  This latter stage also shows a close relationship with sporozoites, whereas first and second generation merozoites are more closely related to each other than to sporozoites.  The profiles were unambiguously associated with the distinct developmental stages and strongly correlated with the order of the stages in the parasite life cycle.  Finally, we present The Eimeria Transcript Database (http://www.coccidia.icb.usp.br/eimeriatdb), a website that provides open access to all sequencing data, annotation and comparative analysis.  We expect this repository to represent a useful resource to the Eimeria scientific community, helping to define potential candidates for the development of new strategies to control coccidiosis of the domestic fowl.