Regions of the genome under positive selection
To investigate positive selection in the P. vivax populations by
country, the genome regions where isolates are identical (referred to as
IBD-segments) was determined by scanning for IBD in 5000 bp windows.
Shared regions of the genome with a high amount of IBD within these
populations can be indicative of positive selection.
Some regions were very similar in many isolates (high proportion of
IBD-sharing), while other regions showed more variety between isolates
(low proportion of IBD sharing; Figure 6A). The IBD-segments that are
shared by the greatest number of isolates are shared by a maximum of 4%
of isolates (Figure 6). While this is a relatively low proportion, this
is as expected from an admixed and recombining parasite population.
The highest amount of IBD-sharing was observed near and in sub-telomeric
regions of the chromosomes, rather than in the core genome. The genes in
regions with the highest amount of IBD-sharing between isolates (peaks
in Figure 6A) in the populations are listed in supplementary table 2.
This includes for example two peaks on chromosome 4 (Figure 6A) that
contain putative genes liver stage antigen 3 (lsa3 ) on the first
peak and Cytosolically Exposed Rhoptry Leaflet Interacting protein 1
(cerli1 ) on the second peak, as well as a region with very little
IBD-sharing (i.e. valley in Figure 6A, in a genomic region with
high genetic variability) containing hypothetical protein PVP01_0424500
(Figure 6A).
Significant IBD segments were investigated for each country resulting in
some regions with significant IBD-sharing in single populations, and
other regions conserved in multiple populations, such as a segment at
the start of chromosome 9 (Figure 6B). Since many chromosomal regions
with significant IBD segments were identified, we investigated the gene
ontologies to determine which pathways were enriched in IBD segments of
the different populations. Enrichment was found in pathways that are
essential for (i ) parasite replication, such as DNA-replication,
binding and repair, protein folding, RNA transcription and processing,
(ii ) transport, (iii ) invasion and antigenic variants,
(e.g. lsa3 , cerli1 , merozoite surface protein 3
(msp3 ), tryptophan-rich proteins (trag6, trag7 ,trag20 )), (iv ) microtubule-related motility, and
(v ) male and female development (supplementary table 2).
No known drug resistance associated genes or orthologues of P.
falciparum resistance associated genes are located in the highest IBD
regions, although dhfr, mdr1 and pvK13 are in areas
with intermediate IBD (Figure 6A). Notably, there is an orthologue of aP. falciparum Kelch interacting protein (kic10 ) in a high
IBD segment on chromosome 9, but the role of this protein and Kelch
proteins in P. vivax drug resistance is unknown.