Malaria.tools: comparative genomic and transcriptomic database for Plasmodium species

Abstract

Malaria is a tropical parasitic disease caused by the Plasmodium genus, which resulted in an estimated 219 million cases of malaria and 435,000 malaria-related deaths in 2017. Despite the availability of the P. falciparum genome since 2002, almost 50% of the genes remain unannotated. To remedy this paucity of functional information, we used transcriptomic data to build gene co-expression networks for two Plasmodium species (P. falciparum and P. berghei), and included genomic data of four other Plasmodium species, P. yoleii, P. knowlesi, P. vivax and P. cynomolgi, as well as two non-Plasmodium species from the Apicomplexa, Toxoplasma gondii and Theileria parva. The database is preloaded with tools that allow the identification and cross-species comparison of co-expressed gene neighborhoods, clusters, and life stage-specific expression, thus providing sophisticated tools to predict gene function. Moreover, we exemplify how the tools can be used to easily identify genes relevant for pathogenicity and various life stages of the malaria parasite. The database is freely available at www.malaria.tools.