{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T23:08:46Z","timestamp":1782083326880,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pgen.1009604","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,1,21]],"date-time":"2022-01-21T00:00:00Z","timestamp":1642723200000}}],"reference-count":88,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T00:00:00Z","timestamp":1641772800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NHMRC Senior Research Fellowship","award":["1102971"],"award-info":[{"award-number":["1102971"]}]},{"name":"Melbourne Research Scholarship"},{"name":"WEHI PhD Scholarship"},{"name":"Victorian State Government Operational Infrastructure Support"},{"name":"Australian Government National Health and Medical Research Council (NHMRC) Independent Research Institute Infrastructure Support Scheme"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    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\n                    <jats:italic>Plasmodium falciparum<\/jats:italic>\n                    and 174\n                    <jats:italic>Plasmodium vivax<\/jats:italic>\n                    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\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    and 3,496 from\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>vivax<\/jats:italic>\n                    ) were used to study\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    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\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    and\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>vivax<\/jats:italic>\n                    have been available in an interactive web-based R Shiny application PlasmoSTR (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/bahlolab\/PlasmoSTR\" xlink:type=\"simple\">https:\/\/github.com\/bahlolab\/PlasmoSTR<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1009604","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T13:28:19Z","timestamp":1641821299000},"page":"e1009604","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4884-1082","authenticated-orcid":true,"given":"Jiru","family":"Han","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2751-0989","authenticated-orcid":true,"given":"Jacob E.","family":"Munro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5924-9466","authenticated-orcid":true,"given":"Anthony","family":"Kocoski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1189-2310","authenticated-orcid":true,"given":"Alyssa E.","family":"Barry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5132-0774","authenticated-orcid":true,"given":"Melanie","family":"Bahlo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,1,10]]},"reference":[{"issue":"6906","key":"pgen.1009604.ref001","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature01097","article-title":"Genome sequence of the human malaria parasite Plasmodium falciparum","volume":"419","author":"MJ Gardner","year":"2002","journal-title":"Nature"},{"issue":"9","key":"pgen.1009604.ref002","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1093\/molbev\/msq108","article-title":"Low-Complexity Regions in Plasmodium falciparum: Missing Links in the Evolution of an Extreme Genome","volume":"27","author":"MM Zilversmit","year":"2010","journal-title":"Molecular Biology and Evolution"},{"issue":"7","key":"pgen.1009604.ref003","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1093\/gbe\/evz140","article-title":"Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment","volume":"11","author":"M McDew-White","year":"2019","journal-title":"Genome Biol Evol"},{"issue":"5","key":"pgen.1009604.ref004","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/S1471-4922(03)00066-7","article-title":"The Plasmodium vivax genome sequencing project","volume":"19","author":"J. 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