TriTrypDB: An integrated functional genomics resource for kinetoplastida

Abstract

Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org). As of release 59, TriTrypDB hosts 83 kinetoplastid genomes, nine of which, including Trypanosoma brucei brucei TREU927, Trypanosoma cruzi CL Brener and Leishmania major Friedlin, undergo manual curation by integrating information from scientific publications, high-throughput assays and user submitted comments. TriTrypDB also integrates transcriptomic, proteomic, epigenomic, population-level and isolate data, functional information from genome-wide RNAi knock-down and fluorescent tagging, and results from automated bioinformatics analysis pipelines. TriTrypDB offers a user-friendly web interface embedded with a genome browser, search strategy system and bioinformatics tools to support custom in silico experiments that leverage integrated data. A Galaxy workspace enables users to analyze their private data (e.g., RNA-sequencing, variant calling, etc.) and explore their results privately in the context of publicly available information in the database. The recent addition of an annotation platform based on Apollo enables users to provide both functional and structural changes that will appear as ‘community annotations’ immediately and, pending curatorial review, will be integrated into the official genome annotation.

LeishMANIAdb: a comparative resource forLeishmaniaproteins

“…number of fragments and missing genes) of their proteome from UniProt [20]. All proteins are also cross-referenced to TriTrypDB [19]. Notably, we noticed that around 30% of the proteins have different sequences deposited into these resources, and in most cases the difference is the position of the initiating Methionine - for data compatibility we always use the UniProt sequence version but the conflicts are highlighted in LeishMANIAdb.…”

“…Protein sequences were retrieved from UniProt [20,27] and from TriTrypDB [19] based on the UniProt cross-references. Homologs in Trypanosomes and in SwissProt were searched with BLAST using e-value: 10 -5 ; sequence identity>20%; coverage>50%.…”

“…We collected high-throughput experiments, predictions and enriched them with manual annotation and structural predictions. Although TriTrypDB [19] also offers some of the datasets we display, it is a genomic resource where individual genes or chromosomal spans can be inspected in their genomic context rather than protein structure and motif information.…”

Non-histone protein methylation inTrypanosoma cruziepimastigotes

“…In order to identify the processes and pathways potentially regulated by methylated proteins in T. cruzi epimastigotes, we performed enrichment analysis of proteins based on Gene Ontology (GO) [39] and KEGG pathways [40] terms available in DAVID [41] and TritrypDB [42] with methylated proteins identified in ≥2 biological replicates. GO analysis revealed a widespread cellular processes and localization of methylated proteins both on nucleus and cytoplasm (Fig.…”

“…The functional classification and enrichment analyses of Gene Ontology (GO) [39] , and Kyoto Encyclopedia of Genes and Genomes (KEGG) [40] were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) tool [41] version 2021 (Dec. 2021) with count 2 and EASE 0.1 and also through TriTrypDB [42] using P-value cuttof 0.05. Protein consensus sequence analyses were performed using k pLogo [43] and iceLogo [44] with the T. cruzi proteome as a reference set.…”