Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Climate-driven niche filtering limits post-dispersal establishment and genomic introgression in a riverine shrub.

Journal of integrative plant biology·2026
Same author

Genome-wide variation in and between two closely related underutilised horsegram species (<i>Macrotyloma axillare</i> and <i>M. uniflorum</i>, Fabaceae).

AoB PLANTS·2026
Same author

Genetic variation and synonymous cultivars in the USDA lychee (<i>Litchi chinensis</i> Sonn.) collection assessed using genome-wide SNPs.

Genetic resources and crop evolution·2025
Same author

Drought Response in the Transcriptome and Ionome of Wild and Domesticated <i>Lablab purpureus</i> L. Sweet, an Underutilized Legume.

Plant-environment interactions (Hoboken, N.J.)·2025
Same author

High Resource Overlap and a Consistently Generalised Pattern of Interactions in a Bat-Flower Network in a Seasonally Dry Landscape.

Ecology and evolution·2024
Same author

Genomics of ecological adaptation in Canary Island <i>Descurainia</i> (Brassicaceae) and comparisons with other Brassicaceae.

Ecology and evolution·2024

Related Experiment Video

Updated: Jan 2, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.5K

Optimizing depth and type of high-throughput sequencing data for microsatellite discovery.

Mark A Chapman1,2

  • 1Biological Sciences University of Southampton Life Sciences Building 85, Highfield Campus Southampton SO17 1BJ United Kingdom.

Applications in Plant Sciences
|December 14, 2019
PubMed
Summary

Discovering simple sequence repeat (SSR) markers using low-cost sequencing is feasible. Transcriptome data yields more SSR markers and transferable primers, while genomic data offers greater variation for species with low polymorphism.

Keywords:
high‐throughput sequencingmarker discoverymicrosatellitessimple sequence repeat (SSR) markers

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.9K

Related Experiment Videos

Last Updated: Jan 2, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.5K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.9K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Simple sequence repeat (SSR) markers, also known as microsatellites, are widely used in genetic research, particularly in resource-limited settings.
  • The optimal sequencing strategy for efficient SSR discovery, comparing genomic versus transcriptomic data, remains underexplored.

Purpose of the Study:

  • To compare the efficacy of SSR identification from plant genomes and transcriptomes at various sequencing depths.
  • To evaluate primer performance, including amplification, polymorphism, and transferability, for SSRs derived from genomic and transcriptomic data.

Main Methods:

  • Utilized high-throughput sequencing data from genomes and transcriptomes at different sequencing depths for SSR discovery.
  • Designed and tested primers from tomato (Solanum lycopersicum) for amplification and polymorphism.
  • Assessed the cross-species transferability of SSR primers to related species.

Main Results:

  • Low-depth sequencing (2 million read pairs) identified hundreds to thousands of potential SSR markers from both genomic and transcriptomic assemblies.
  • Transcriptome assemblies yielded a higher number of SSRs and longer contigs, facilitating primer design.
  • Genomic SSR primers showed less interspecific transferability but greater variation compared to transcriptome-derived primers.

Conclusions:

  • Limited high-throughput sequencing resources are adequate for substantial SSR marker discovery.
  • Transcriptomic SSRs are generally more suitable for primer design and exhibit broader transferability.
  • Genomic SSRs may be advantageous in species with low inherent polymorphism due to higher variability.