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

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

3.7K
By running the Pathway Association Study Tool (PAST), either through the Shiny application or through the R console, researchers can gain a deeper understanding of the biological meaning of their genome-wide association study (GWAS) results by investigating the metabolic pathways involved.
3.7K
Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses12:20

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

22.0K
Here, a protocol is presented for creating an infectious bacterial artificial chromosome containing a full-length cDNA of the positive-strand genomic RNA of Japanese encephalitis virus. This protocol can be used to construct a functional cDNA of other positive-strand RNA viruses, making it a powerful genomic tool for studying virus...
22.0K
Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

11.6K
A mass spectrometry-guided genome mining protocol is established and described here. It is based on genome sequence information and LC-MS/MS analysis and aims to facilitate identification of molecules from complex microbial and plant...
11.6K
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA12:36

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

10.6K
We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of...
10.6K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

411.6K
The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.
411.6K
Genetic Manipulation of the Plant Pathogen Ustilago maydis to Study Fungal Biology and Plant Microbe Interactions11:42

Genetic Manipulation of the Plant Pathogen Ustilago maydis to Study Fungal Biology and Plant Microbe Interactions

15.1K
We describe a robust gene replacement strategy to genetically manipulate the smut fungus Ustilago maydis. This protocol explains how to generate deletion mutants to investigate infection phenotypes. It can be extended to modify genes in any desired way, e.g., by adding a sequence encoding a fluorescent protein...
15.1K

You might also read

Related Articles

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

Sort by
Same author

Plastome evolution and phylogenomic relationships in Ajuga (Lamiaceae, Ajugoideae).

BMC plant biology·2026
Same author

A comprehensive phylogenomic framework for cycads (Cycadales).

PhytoKeys·2026
Same author

A Comparison of Volatile Components Across Native Australian Mentha (Lamiaceae).

Plants (Basel, Switzerland)·2026
Same author

Trust and Perceived Trustworthiness in Health-Related Data Sharing Among UK Adults: Cross-Sectional Survey.

Journal of medical Internet research·2025
Same author

Low genetic differentiation among morphologically distinct Cycas species informs the delineation of conservation management units.

Annals of botany·2025
Same author

Demonstration of the Use of NSGA-II for Optimization of Sparse Acoustic Arrays.

Sensors (Basel, Switzerland)·2025

Related Experiment Video

Updated: Jan 20, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.7K

RADseq as a valuable tool for plants with large genomes-A case study in cycads.

James A R Clugston1,2, Gregory J Kenicer2, Richard Milne1

  • 1School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.

Molecular Ecology Resources
|September 5, 2019
PubMed
Summary

Restriction site-associated DNA sequencing (RADseq) successfully generated numerous genome-wide markers for cycads, ancient plants with very large genomes. This cost-effective method provides valuable data for studying these unique species.

Keywords:
RADseqcycadsillumina sequencinglarge genomes

More Related Videos

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
12:20

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Published on: December 29, 2015

22.0K
Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.6K

Related Experiment Videos

Last Updated: Jan 20, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.7K
Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
12:20

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Published on: December 29, 2015

22.0K
Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.6K

Area of Science:

  • Genomics
  • Plant Science
  • Evolutionary Biology

Background:

  • Full genome sequencing is challenging and expensive for organisms with large, complex genomes, such as cycads (Cycadales), which possess genomes up to 60 Gbp.
  • Restriction site-associated DNA sequencing (RADseq) is a cost-effective method for identifying genome-wide markers in various organisms.

Purpose of the Study:

  • To evaluate the effectiveness of RADseq, specifically the ezRAD protocol, for generating genome-wide markers across all 10 genera of Cycadales.
  • To adapt and apply RADseq to cycads, overcoming challenges posed by their large genomes and high plastid numbers.

Main Methods:

  • Applied ezRAD protocol to samples from all 10 Cycadales genera, including a specific dataset for Cycas calcicola (72 samples).
  • Utilized existing plastid and mitochondrial genomes for read mapping to recover genomic regions.
  • Performed de novo assembly to identify phylogenetically informative nuclear loci.

Main Results:

  • Successfully recovered plastid, mitochondrial, and nuclear markers across all cycad genera.
  • De novo assembly yielded up to 138,407 high-depth clusters and 1,705 informative loci per genus, with 4,421 loci for C. calcicola.
  • Marker numbers were sufficient for downstream analyses and could be increased by adjusting assembly parameters.

Conclusions:

  • Demonstrated the successful application of RADseq for generating a substantial number of genome-wide markers in cycads, despite their large genomes.
  • The modified RADseq protocol is suitable for cycads and other organisms with large genomes, providing a valuable tool for genetic and evolutionary studies.