title: A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.
abstract: OBJECTIVE
  The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.
  
  
  RESULTS
  Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.
  
  
  CONCLUSIONS
  We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.
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: Department of Biology, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
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: 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; 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: Jacob B
authors.initials: JB
authors.lastname: Landis
authors.affiliation: Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador.
authors.forename: M Claudia
authors.initials: MC
authors.lastname: Segovia-Salcedo
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Norman A
authors.initials: NA
authors.lastname: Douglas
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: 1KP; microsatellite development; neutral markers; next-generation sequencing (NGS); non-neutral markers; simple sequence repeat (SSR); transcriptomes