EuPathDB: The Eukaryotic Pathogen database

Abstract

EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNA-seq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010.

The Role of Palmitoylation for Protein Recruitment to the Inner Membrane Complex of the Malaria Parasite

“…The apicomplexan organisms used for this analysis are as follows: Cryptosporidium hominis TU502; Cryptosporidium muris RN66; Cryptosporidium parvum IowaII; Babesia bovis T2Bo; Theileria annulata strain Ankara; Theileria parva strain Muguga; P. berghei ANKA; Plasmodium chabaudi chabaudi, Plasmodium cynomolgi strain B; P. falciparum 3D7; Plasmodium knowlesi strain H; Plasmodium vivax Sal-1; Plasmodium yoelii yoelii 17XNL; Neospora caninum Liverpool; T. gondii ME49; Eimeria tenella strain Houghton, and their proteomes were downloaded from EupathDB (37). The hits were then manually checked for the presence of cysteine-rich domain (CRD), an ϳ50-amino acid region housing the catalytically active DHH(Y)C residues (38).…”

Leishmania donovani Encodes a Functional Selenocysteinyl-tRNA Synthase

“…3) clearly shows that the kinetoplastid SepSecS enzymes are phylogenetically closer to worm SepSecS, whereas the metazoan enzymes are closer to fly and plant SepSecS enzymes. The Plasmodium and L. braziliensis SepSecS could not be retrieved by a simple BLAST search in the EupathDB database (35,36) using the human SepSecS query sequence. Although, Plasmodium homologs are retrieved by a specific BLAST search in PlasmoDB database, the L. braziliensis SepSecS is retrieved by orthology to other Leishmania species.…”

Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attack

“…Proteome fi les were downloaded from Uniprot ( 22 ), EuPathDB ( 23 ), and Integr8 ( 24 ). The predicted proteomes were tested for completeness against the 100 most conserved proteins of the Core Eukaryotic Genes Mapping Approach database ( 25 ), which we had determined based on HMMer 3.0 profi le ( 26,27 ) searches of eukaryote reference proteomes ( C. elegans , inhibitors (SBIs) are widely deployed as chemotherapeutics.…”