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Microsatellites are a powerful tool in population genetics and phylogeographic analysis. However, only a few microsatellite markers were reported in<jats:italic>T. spiralis<\/jats:italic>. Thus, there is a need to develop and validate genome-wide microsatellite markers for<jats:italic>T. spiralis<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Microsatellites were selected from shotgun genomic sequences using MIcroSAtellite identification tool (MISA). The identified markers were validated in 12 isolates of<jats:italic>T. spiralis<\/jats:italic>in China.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 93,140 microsatellites were identified by MISA from 9267 contigs in<jats:italic>T. spiralis<\/jats:italic>genome sequences, in which 16 polymorphic loci were selected for validation by PCR with single larvae from 12 isolates of<jats:italic>T. spiralis<\/jats:italic>in China. There were 7\u201319 alleles per locus (average 11.25 alleles per locus). The observed heterozygosity (<jats:italic>H<\/jats:italic><jats:sub><jats:italic>O<\/jats:italic><\/jats:sub>) and expected heterozygosity (<jats:italic>H<\/jats:italic><jats:sub><jats:italic>E<\/jats:italic><\/jats:sub>) ranged from 0.325 to 0.750 and 0.737 to 0.918, respectively. The polymorphism information content (PIC) ranged from 0.719 to 0.978 (average 0.826). Among the 16 loci, markers for 10 loci could be amplified from all 12 international standard strains of<jats:italic>Trichinella<\/jats:italic>spp.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Sixteen highly polymorphic markers were selected and validated for<jats:italic>T. spiralis<\/jats:italic>. Primary phylogenetic analysis showed that these markers might serve as a useful tool for genetic studies of<jats:italic>Trichinella<\/jats:italic>parasites.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-020-3929-2","type":"journal-article","created":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T16:02:50Z","timestamp":1581436970000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis"],"prefix":"10.1186","volume":"13","author":[{"given":"Ting-Ting","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue","family":"Bai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue-Lin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue-Nong","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong-Bin","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong-Fei","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Jia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Lei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming-Yuan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,2,11]]},"reference":[{"key":"3929_CR1","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1016\/j.ijpara.2013.05.010","volume":"43","author":"E Pozio","year":"2013","unstructured":"Pozio E, Zarlenga DS. 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