The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

Abstract

Parasites of the genus Eimeria infect a wide range of vertebrate hosts, including chickens. We have recently reported a comparative analysis of the transcriptomes of Eimeria acervulina, Eimeria maxima and Eimeria tenella, integrating ORESTES data produced by our group and publicly available Expressed Sequence Tags (ESTs). All cDNA reads have been assembled, and the reconstructed transcripts have been submitted to a comprehensive functional annotation pipeline. Additional studies included orthology assignment across apicomplexan parasites and clustering analyses of gene expression profiles among different developmental stages of the parasites. To make all this body of information publicly available, we constructed the Eimeria Transcript Database (EimeriaTDB), a web repository that provides access to sequence data, annotation and comparative analyses. Here, we describe the web interface, available sequence data sets and query tools implemented on the site. The main goal of this work is to offer a public repository of sequence and functional annotation data of reconstructed transcripts of parasites of the genus Eimeria. We believe that EimeriaTDB will represent a valuable and complementary resource for the Eimeria scientific community and for those researchers interested in comparative genomics of apicomplexan parasites.Database URL: http://www.coccidia.icb.usp.br/eimeriatdb/

Two COWP-like cysteine rich proteins from Eimeria nieschulzi (coccidia, apicomplexa) are expressed during sporulation and involved in the sporocyst wall formation

“…The putative amino acid sequence in the last protein encoding exon was identified by similarity of the distance of cysteine encoding triplets and the occurrence of a stop codon in the same open reading frame, as well as the absence of putative splice donor sites. The identified, putative protein sequences were again analyzed by TBLASTN against predicted proteins in Eimeria species at GenBank and ToxoDB ([ 13 ] as well as in transcripts deposited at Eimeria Transcript database [ 14 , 15 ]).…”

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

“…To harvest additional related sequences, the DDBJ/EMBL/GenBank non-redundant protein database was searched using Hidden–Markov Models built from all reference sequences from each group with HMMER (Eddy, 2009). These results were obtained from the December 2010 release of FunGene (http://fungene.cme.msu.edu, see also Fish et al, 2013). An HMM bits saved score cutoff of 700 was used, and no additional sequences were obtained through this search, which reinforces the low number of sequenced (or cultured) strains with activity toward dibenzo- p -dioxin.…”

Toxoplasma gondii immune mapped protein 1 is anchored to the inner leaflet of the plasma membrane and adopts a novel protein fold

“…TgIMP1 is expressed in all life stages of T. gondii except in merozoites [25] and the raw data from Eimeria transcript Database indicates two expression peaks appearing in the stage of sporulated oocysts and during the second generation of the merozoites in E. tenella [26]. Although disruption of the TgIMP1 in tachyzoites showed no loss of parasite fitness, a role in other stages as well as redundancy between members of this family of proteins cannot be excluded.…”