ArticleApplications in plant sciences2016
A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.
Article in Applications in plant sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 36 citations in OpenAlex.
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- Efficient PCR Amplification Protocol of Nuclear Microsatellites for Exuviae-Derived DNA of Cicada,Frontiers in insect science · 2021Article
- Comparative analysis of genomic- and EST-SSRs in European plum (3 Biotech · 2020Article
- Optimizing depth and type of high-throughput sequencing data for microsatellite discovery.Applications in plant sciences · 2019Article
- Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae).BMC plant biology · 2019Article
- Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data.BMC genomics · 2018Article
- Article
- Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering.Scientific reports · 2017Article
- Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Applications in plant sciences · 2017Article
- Development and characterization of EST-SSR markers inApplications in plant sciences · 2017Article
- Transcriptomic resources and marker validation for diploid and polyploidApplications in plant sciences · 2016Article
- The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.Applications in plant sciences · 2016Article
- A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.Applications in plant sciences · 2016Article
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyThe 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
resultsUsing 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.
conclusionsWe 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.
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