title: The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.
abstract: Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Richard G J
authors.initials: RG
authors.lastname: Hodel
authors.affiliation: Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas-ESPE, Sangolqui, Ecuador.
authors.forename: M Claudia
authors.initials: MC
authors.lastname: Segovia-Salcedo
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Jacob B
authors.initials: JB
authors.lastname: Landis
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Crowl
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Sun
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Xiaoxian
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Norman A
authors.initials: NA
authors.lastname: Douglas
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Charlotte C
authors.initials: CC
authors.lastname: Germain-Aubrey
authors.affiliation: College of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Shichao
authors.initials: S
authors.lastname: Chen
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
keywords: genotyping by sequencing (GBS); microsatellite development; next-generation sequencing (NGS); restriction site associated DNA sequencing (RAD-Seq); simple sequence repeats (SSR); transcriptomes