Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species

Han, J; Munro, JE; Kocoski, A; Barry, AE; Bahlo, M

Author(s): Han, J; Munro, JE; Kocoski, A; Barry, AE; Bahlo, M;
Details: Publication Year 2022-01,Volume 18,Issue #1,Page e1009604
Journal Title: PLoS Genetics
Abstract: 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 3,000 Plasmodium falciparum and 174 Plasmodium vivax published 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 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic 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 in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
Publisher: PLOS
Research Division(s): Population Health And Immunity
PubMed ID: 35007277
Publisher's Version: https://doi.org/10.1371/journal.pgen.1009604
Open Access at Publisher's Site: https://doi.org/10.1371/journal.pgen.1009604
Terms of Use/Rights Notice: Refer to copyright notice on published article.
Documents: journal.pgen.1009604.pdf - (1.70MB, application/pdf)

Creation Date: 2022-02-16 10:11:25

Last Modified: 2022-02-16 10:11:56