Characterization of P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms

Adam Kim,Sócrates Herrera,Camille Roesch,David Serre,Didier Ménard,Sophalai Bin,Myriam Arévalo-Herrera,Philip Felgner,Reingsey Samreth,Saorin Kim,Amélie Vantaux,Huw Davies,Jean Popovici,Li Liang

doi:10.1038/s41598-017-07275-9

Abstract

Our understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures. Most P. vivax studies must therefore rely on patient samples, which typically display a low proportion of parasites and asynchronous parasites. Here, we present stranded RNA-seq data generated directly from a small volume of blood from three Cambodian vivax malaria patients collected before treatment. Our analyses show surprising similarities of the parasite gene expression patterns across infections, despite extensive variations in parasite stage proportion. These similarities contrast with the unique gene expression patterns observed in sporozoites isolated from salivary glands of infected Colombian mosquitoes. Our analyses also indicate that more than 10% of P. vivax genes encode multiple, often undescribed, protein-coding sequences, potentially increasing the diversity of proteins synthesized by blood stage parasites. These data also greatly improve the annotations of P. vivax gene untranslated regions, providing an important resource for future studies of specific genes.

Highlights

Our understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures
While investigations in P. falciparum are essential for characterizing fundamental mechanisms of gene regulation of Plasmodium parasites, they are unlikely to be sufficient for understanding specific biological features of other human malaria parasites
We describe for the first time, analyses of P. vivax transcriptomes directly generated from 50 uL of capillary blood collected from three Cambodian vivax malaria patients

Summary

Introduction

Our understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures. Our analyses show surprising similarities of the parasite gene expression patterns across infections, despite extensive variations in parasite stage proportion. Our analyses indicate that more than 10% of P. vivax genes encode multiple, often undescribed, protein-coding sequences, potentially increasing the diversity of proteins synthesized by blood stage parasites. These data greatly improve the annotations of P. vivax gene untranslated regions, providing an important resource for future studies of specific genes. Most studies of gene expression in Plasmodium parasites have been conducted using P. falciparum, due to its public health importance and its ability to be grown in vitro, which i) facilitates acquisition of study material, ii) enables synchronization of the parasite stages, and iii) provides a controlled (though artificial) environment. We compared the gene expression profiles of blood stage parasites with those of sporozoites to further expand our understanding of P. vivax genes and their regulation

Methods

Results

Conclusion