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Background   Plasmodium falciparum  exhibits a high degree of inter-isolate genetic diversity in its variant surface antigen (VSA) families:  P. falciparum  erythrocyte membrane protein 1, repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR). The role of recombination for the generation of this diversity is a subject of ongoing research. Here the genome of E5, a sibling of the 3D7 genome strain is presented. Short and long read whole genome sequencing (WGS) techniques (Ilumina, Pacific Bioscience) and a set of 84 microsatellites (MS) were employed to characterize the 3D7 and non-3D7 parts of the E5 genome. This is the first time that VSA genes in sibling parasites were analysed with long read sequencing technology.    Results  Of the 5733 E5 genes only 278 genes, mostly  var  and  rifin/stevor  genes, had no orthologues in the 3D7 genome. WGS and MS analysis revealed that chromosomal crossovers occurred at a rate of 0–3 per chromosome.  var, stevor  and  rifin  genes were inherited within the respective non-3D7 or 3D7 chromosomal context. 54 of the 84 MS PCR fragments correctly identified the respective MS as 3D7- or non-3D7 and this correlated with  var  and  rifin/stevor  gene inheritance in the adjacent chromosomal regions. E5 had 61  var  and 189  rifin/stevor  genes. One large non-chromosomal recombination event resulted in a new  var  gene on chromosome 14. The remainder of the E5 3D7-type subtelomeric and central regions were identical to 3D7.    Conclusions  The data show that the  rifin/stevor  and  var  gene families represent the most diverse compartments of the  P. falciparum  genome but that the majority of  var  genes are inherited without alterations within their respective parental chromosomal context. Furthermore, MS genotyping with 54 MS can successfully distinguish between two sibling progeny of a natural  P. falciparum  cross and thus can be used to investigate identity by descent in field isolates.    Electronic supplementary material  The online version of this article (10.1186/s12936-018-2503-2) contains supplementary material, which is available to authorized users.

malaria journal

Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance