A New Resource for the Development of SSR Markers: Millions of Loci from a Thousand Plant Transcriptomes

Premise of the study: 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. Methods and Results: U...

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Published inApplications in plant sciences Vol. 4; no. 6
Main Authors Hodel, Richard G. J, Gitzendanner, Matthew A, Germain-Aubrey, Charlotte C, Liu, Xiaoxian, Crowl, Andrew A, Sun, Miao, Landis, Jacob B, Segovia-Salcedo, M. Claudia, Douglas, Norman A, Chen, Shichao, Soltis, Douglas E, Soltis, Pamela S
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America 01.06.2016
John Wiley & Sons, Inc
Subjects
1KP
computer software
cost effectiveness
Datasets
DNA
Exons
Flowers & plants
Gene loci
Genomes
GENOMIC RESOURCES NOTE
loci
microsatellite development
microsatellite repeats
Microsatellites
neutral markers
next-generation sequencing (NGS)
non-neutral markers
Nucleotide sequence
Open reading frames
Plant sciences
polymerase chain reaction
Researchers
Scripts
simple sequence repeat (SSR)
Software packages
Studies
transcriptome
transcriptomes
transcriptomics
translation (genetics)
microsatellite development
1KP
next-generation sequencing (NGS)
non-neutral markers
simple sequence repeat (SSR)
transcriptomes
neutral markers
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Summary:Premise of the study: 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. Methods and 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.
Bibliography:The authors thank Gane Ka‐Shu Wong and the One Thousand Plant Transcriptomes Project (1KP) for graciously allowing us to use the assembled scaffolds of 1334 plant transcriptomes, and we thank three anonymous reviewers and
associate editor Dr. Mitch Cruzan for their helpful comments on previous versions of this manuscript. This work was supported in part by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB‐1501600 to D.E.S. and R.G.J.H.).
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The authors thank Gane Ka-Shu Wong and the One Thousand Plant Transcriptomes Project (1KP) for graciously allowing us to use the assembled scaffolds of 1334 plant transcriptomes, and we thank three anonymous reviewers and APPS associate editor Dr. Mitch Cruzan for their helpful comments on previous versions of this manuscript. This work was supported in part by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB-1501600 to D.E.S. and R.G.J.H.).
ISSN:2168-0450
2168-0450
DOI:10.3732/apps.1600024