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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.4K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.4K
RNA-seq03:21

RNA-seq

10.5K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.5K

You might also read

Related Articles

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

Sort by
Same author

Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.

American journal of botany·2026
Same author

Phylogenomics of Melastomataceae: rooting out discordance across organellar and nuclear genomes.

Molecular phylogenetics and evolution·2026
Same author

Genomic structure and functional trait variation are decoupled across the Atacama-Patagonia arid gradient in the Chilean wineberry.

Frontiers in plant science·2026
Same author

A chromosome-level genome assembly of the beavertail cactus, Opuntia basilaris.

The Journal of heredity·2025
Same author

The PteridoPortal: A publicly accessible collection of over three million records of extant and extinct pteridophytes.

Applications in plant sciences·2025
Same author

Evolution of the Xerocarpa clade (<i>Opuntia</i>; Opuntieae): Evidence for the Role of the Grand Canyon in the Biogeographic History of the Iconic Beavertail Cactus and Relatives.

Plants (Basel, Switzerland)·2023

Related Experiment Video

Updated: Oct 2, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.8K

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.

Serena Acha1, Lucas C Majure1

  • 1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.

Genes
|February 25, 2022
PubMed
Summary

This study introduces a new targeted sequence capture method to resolve cactus (Cactaceae) evolutionary relationships. Combining custom and universal probe sets significantly improves phylogenetic resolution, especially at the genus level.

Keywords:
Hyb-seqOpuntiacactineotropicstarget enrichment

More Related Videos

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
09:48

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Published on: April 22, 2022

4.2K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.6K

Related Experiment Videos

Last Updated: Oct 2, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.8K
Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
09:48

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Published on: April 22, 2022

4.2K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.6K

Area of Science:

  • Botany
  • Evolutionary Biology
  • Genomics

Background:

  • Chloroplast DNA data have largely resolved major cactus (Cactaceae) clades.
  • However, nuclear genome data are needed to clarify relationships at deeper phylogenetic nodes and at the generic and species levels.

Purpose of the Study:

  • To develop and test a targeted sequence capture approach using nuclear markers to improve phylogenetic resolution within Cactaceae.
  • To compare the effectiveness of a custom Cactaceae-specific probe set with the Angiosperms353 probe set.

Main Methods:

  • Designed a custom Cactaceae probe set using MarkerMiner and combined it with the Angiosperms353 probe set.
  • Applied a targeted sequence capture pipeline to 36 transcriptomes and 96 accessions (88 species) of Cactaceae.
  • Reconstructed phylogenies using Hybpiper, RAxML-NG, and Astral, analyzing nuclear and plastome data.

Main Results:

  • A well-supported phylogeny for Cactaceae was recovered, largely congruent with plastome data for major clades.
  • Incongruences were observed between nuclear and plastome datasets, particularly at the generic level, highlighting the value of nuclear markers.
  • The combined probe set approach showed significant potential for enhancing phylogenetic resolution.

Conclusions:

  • Targeted sequence capture using a combination of Cactaceae-specific and universal probe sets is a powerful tool for resolving cactus phylogeny.
  • Nuclear markers provide complementary and sometimes conflicting information compared to plastome data, crucial for resolving complex evolutionary histories.
  • This approach has broad applicability for phylogenetic studies in other plant families.