PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

Frank Schwach,Colin Herd,Oliver Billker,Ana Rita Gomes,Burcu Anar,Ellen Bushell,Julian C Rayner,Gareth Girling

doi:10.1093/nar/gku1143

Frank Schwach, Colin Herd + Show 6 more

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https://doi.org/10.1093/nar/gku1143

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Journal: Nucleic acids research	Publication Date: Jan 28, 2015
Citations: 98	License type: CC BY 4.0

Affiliation: Wellcome Sanger Institute

Abstract

The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves.

Highlights

Malaria is caused by parasites of the genus Plasmodium, members of which have adapted to infect a wide range of vertebrate hosts
The extremely high content of adenine and thymine nucleotides (>77%) poses significant additional challenges to scaling up manipulation of the genome because it renders P. berghei genomic DNA unstable in E. coli. The latter problem can be overcome in part by using a new class of low copy linear plasmid derived from phage N15 [2], which has allowed the generation of a representative genomic library covering most P. berghei genes in their entirety to be maintained in E. coli for the first time [3]
Since recombineering technology is robust and scalable, but not generally established in parasitology laboratories, we have initiated the Plasmodium Genetic Modification Project (PlasmoGEM), which has at its heart a production pipeline for a genome wide community resource of barcoded genetic modification vectors

Summary

Introduction

Malaria is caused by parasites of the genus Plasmodium, members of which have adapted to infect a wide range of vertebrate hosts. Since recombineering technology is robust and scalable, but not generally established in parasitology laboratories, we have initiated the Plasmodium Genetic Modification Project (PlasmoGEM), which has at its heart a production pipeline for a genome wide community resource of barcoded genetic modification vectors.

Results

Conclusion