Population-level genome-wide STR typing inPlasmodiumspecies reveals higher resolution population structure and genetic diversity relative to SNP typing
Authors: Han Jiru , Munro Jacob E. , Kocoski Anthony , Barry Alyssa E. , Bahlo Melanie 
Published: May 2021

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000Plasmodium falciparumand 174Plasmodium vivaxpublished whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 fromP. falciparumand 3,496 fromP. vivax) were used to studyPlasmodiumgenetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs inP. falciparumandP. vivaxhave been made available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

Author summary

Malaria is a severe disease caused by a genus of parasites calledPlasmodiumand is transmitted to humans through infectedAnophelesmosquitoes.P. falciparumandP. vivaxare the predominant species responsible for more than 95% of all human malaria infections which continue to pose a significant challenge to human health. Antimalarial drug resistance is a serious threat hindering the elimination of malaria. As such, it is important to understand the role of genomic variation in the development of antimalarial drug resistance. STRs are an important source of genomic variation that, from a population genetics perspective, have several advantages over SNPs, including being highly polymorphic, having a higher mutation rate, and having been widely used to study the population structure and genetic diversity. However, STRs are not routinely genotyped with bioinformatic tools across the whole genome with short read sequencing data because they are difficult to identify and genotype accurately, as they vary in size and may align poorly to the reference genome, therefore requiring rigorous quality control (QC). In this study, we genotype STRs using HipSTR[1] in more than 3,000P. falciparumand 174P. vivaxwhole-genome sequence samples collected world-wide. We develop a multivariable logistic regression model for the measurement and prediction of the quality of STRs. In addition, we use a set of genome-wide high-quality STRs to study parasite population genetics and compare them to genome-wide SNP genotyping data, revealing both high consistency with SNP based signals, as well as identifying some signals unique to the STR marker data. These results demonstrate that the identification of highly informative STR markers from large numbers of population samples is a powerful approach to study the genetic diversity, population structures and genomic signatures of selection inP. falciparumandP. vivax. Furthermore, we built an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR) that includes genome-wide information about genetic variation and other characteristics of the high quality STRs identified inP. falciparumandP. vivax, allowing researchers to explore and visualize the specific STRs.