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Abstract
Two decades after the first Plasmodium transfection, attempts have been made to disrupt more than 3,151 genes in malaria parasites, across five Plasmodium species. While results from rodent malaria transfections have been curated and systematised, empowering large-scale analysis, phenotypic data from human malaria parasite transfections currently exists as individual reports scattered across a the literature. To facilitate systematic analysis of published experimental genetic data across Plasmodium species, we have built PhenoPlasm ( http://www.phenoplasm.org), a database of phenotypes generated by transfection experiments in all Plasmodium parasites. The site provides a simple interface linking citation-backed Plasmodium reverse-genetic phenotypes to gene IDs. The database has been populated with phenotypic data on 367 P. falciparum genes, curated from 176 individual publications, as well as existing data on rodent Plasmodium species from RMgmDB and PlasmoGEM. This is the first time that all available data on P. falciparum transfection experiments has been brought together in a single place. These data are presented using ortholog mapping to allow a researcher interested in a gene in one species to see results across other Plasmodium species. The collaborative nature of the database enables any researcher to add new phenotypes as they are discovered. As an example of database utility, we use the currently available datasets to identify RAP (RNA-binding domain abundant in Apicomplexa)-domain containing proteins as crucial to parasite survival.
Highlights
The increasing use of experimental genetics in Plasmodium spp. has provided numerous insights into the biology of the malaria parasite
To facilitate systematic analysis of published experimental genetic data across Plasmodium species, we have built PhenoPlasm, a database of phenotypes generated by transfection experiments in all Plasmodium parasites
The database has been populated with phenotypic data on 367 P. falciparum genes, curated from 176 individual publications, as well as existing data on rodent Plasmodium species from RMgmDB and PlasmoGEM
Summary
The increasing use of experimental genetics in Plasmodium spp. has provided numerous insights into the biology of the malaria parasite (de Koning-Ward et al, 2015) To date such results for P. falciparum transfection experiments are scattered across a range of journals, with no unified or queryable interface. The rodent malaria genetically modified parasite database (RMgmDB, http://pberghei.eu; Khan et al, 2013) provides a powerful curated resource for the rodent Plasmodium species, and contains curated data on disruption attempts for over 500 genes from individual studies, making it the largest manually curated database for Plasmodium experimental genetic data. While some human Plasmodium parasite genes lack rodent orthologs, nearly 75% have such orthologs, and integrating human and rodent Plasmodium phenotypes is likely to be highly informative To allow such integration, any new database schema must be compatible with that of RMgmDB, which is broken into 6 different stages at which phenotypes can occur (asexual, gametocyte/gamete, fertilization & ookinete, oocyst, sporozoite and liver). The database must import phenotypes from the largest source of blood stage Plasmodium phenotyping data available to date, PlasmoGEM barcode-sequencing experiments (Bushell et al, 2017)
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