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

DNA-only Transposons02:57

DNA-only Transposons

14.6K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.6K
DNA Microarrays02:34

DNA Microarrays

17.9K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
17.9K
DNA Isolation01:24

DNA Isolation

39.6K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
39.6K

You might also read

Related Articles

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

Sort by
Same author

Harnessing the murine inner cell mass mechanical environment enhances derivation of in vitro nascent primitive endoderm precursor cells.

Development (Cambridge, England)·2026
Same author

Combined phylogenetic and geographic data can predict plant-pest interactions with high accuracy.

The New phytologist·2026
Same author

randPedPCA: rapid approximation of principal components from large pedigrees.

Genetics, selection, evolution : GSE·2025
Same author

Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic.

Science (New York, N.Y.)·2025
Same author

Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding.

Nature communications·2025
Same author

Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function.

Genes & development·2025
Same journal

From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.

Molecular ecology resources·2026
Same journal

EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.

Molecular ecology resources·2026
Same journal

A Practical Framework for GT-Seq Panel Optimization.

Molecular ecology resources·2026
Same journal

Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.

Molecular ecology resources·2026
Same journal

pr2-Wormifier: A Bioinformatics Pipeline to Create Custom Reference Databases for Improved Metabarcoding of Marine Protists.

Molecular ecology resources·2026
Same journal

Individual Identification of Prey in Carnivore Scats.

Molecular ecology resources·2026
See all related articles

Related Experiment Video

Updated: Aug 11, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

320

Assembly-free quantification of vagrant DNA inserts.

Hannes Becher1, Richard A Nichols2

  • 1Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.

Molecular Ecology Resources
|February 6, 2023
PubMed
Summary
This summary is machine-generated.

Scientists developed new statistical methods to quantify nuclear DNA inserts from extranuclear sources, like mitochondria. These methods use low-coverage sequencing data, enabling accurate abundance estimation even without a full nuclear genome assembly.

Keywords:
NUMTsNUPTsendosymbiontsgenome skimmingnuclear pseudogenesquantification

More Related Videos

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

12.6K
Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

17.3K

Related Experiment Videos

Last Updated: Aug 11, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

320
Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

12.6K
Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

17.3K

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Eukaryotic nuclear genomes frequently contain DNA inserts from extranuclear sources (organelles, microbes).
  • Challenges in genome assembly due to sequence similarity and multiple insertions hinder accurate quantification of these vagrant DNAs.
  • Existing methods struggle to reliably infer the number, sequence, and location of these nuclear inserts.

Purpose of the Study:

  • To introduce novel statistical methods for estimating the abundance of nuclear DNA inserts from extranuclear sources.
  • To enable quantification of these inserts even without a complete nuclear genome assembly.
  • To provide tools for analyzing low-coverage sequencing data for vagrant DNA quantification.

Main Methods:

  • Development of two statistical methods: the 'intercept method' using low-coverage sequencing data (<1×) and a second method requiring diverged extranuclear DNA genotypes in a subset of individuals.
  • Validation of the intercept method through simulations and re-estimation of human nuclear mitochondrial inserts (NUMTs).
  • Application of the intercept method to estimate NUMT abundance in the grasshopper Podisma pedestris and museomics data from the parrot Psephotellus varius.

Main Results:

  • The intercept method accurately estimates nuclear insert abundance using low-coverage sequencing data.
  • In Podisma pedestris, NUMTs constitute 0.056% of the nuclear genome, exceeding mitochondrial genome size by over 500 times.
  • In Psephotellus varius, NUMTs represent 0.0043% of the nuclear genome, consistent with avian data.

Conclusions:

  • Low-coverage high-throughput sequencing data are effective for quantifying nuclear vagrant DNAs.
  • The developed statistical methods, implemented in the R package 'vagrantDNA', are versatile for quantifying organellar and endosymbiont-derived sequences.
  • These methods overcome assembly limitations, providing reliable estimates of nuclear insert abundance across diverse organisms.