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

5.7K
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...
5.7K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.9K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.7K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.1K
Next-generation Sequencing03:00

Next-generation Sequencing

88.8K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.8K

You might also read

Related Articles

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

Sort by
Same author

Single-cell analyses of tissue regeneration in two true jellyfish.

Molecular biology and evolution·2026
Same author

A Flexible Method for Genomics-Based Quantitative Genetics in Wild Study Systems-A Case Study on a House Sparrow Meta-Population.

Evolutionary applications·2026
Same author

Population-scale interpretation of RNA isoform diversity enabled by Isopedia.

bioRxiv : the preprint server for biology·2026
Same author

Seasonal timing in a changing world: the epigenetic link between environment and reproduction across taxa.

Environmental epigenetics·2026
Same author

Spatial heterogeneity in density dependence across life-history stages drives the dynamics of a bird metapopulation.

Ecology·2026
Same author

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom.

NAR genomics and bioinformatics·2026
Same journal

Evidence for cryptic sex in Escovopsis, a mycoparasite in the fungus-growing ant symbiosis.

Genome biology and evolution·2026
Same journal

Experimental evolution under biased sex ratios: phenotypic and genomic responses in the bulb mite, Rhizoglyphus robini.

Genome biology and evolution·2026
Same journal

Optimal organelle inheritance strategies under different changing environments and mutational pressures.

Genome biology and evolution·2026
Same journal

A reassessment of positive growth effects of expressed random sequence clones in E. coli suggests direct adaptive functions.

Genome biology and evolution·2026
Same journal

Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder (Vipera berus).

Genome biology and evolution·2026
Same journal

Exploring the determinants of polydnavirus chromosomal integration across host-parasitoid wasp systems.

Genome biology and evolution·2026
See all related articles

Related Experiment Video

Updated: Jun 30, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

962

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

Gabriel David1, Alicia Bertolotti2, Ryan Layer3,4

  • 1Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

Genome Biology and Evolution
|March 15, 2024
PubMed
Summary
This summary is machine-generated.

High-confidence structural variant callsets are crucial for population genomics. Manual curation of short-read data significantly reduces false positives, improving variant accuracy and enabling robust population structure analysis.

Keywords:
curation strategieshigh-confidence variantsputative false positivesrapid manual curationshort readsstructural variation

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

15.2K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

8.6K

Related Experiment Videos

Last Updated: Jun 30, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

962
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

15.2K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

8.6K

Area of Science:

  • Population genomics
  • Genomic variation analysis
  • Bioinformatics

Background:

  • Characterizing structural variation in natural populations is a recent advancement.
  • High-confidence structural variant callsets are essential for population genomic studies.
  • Short-read sequencing data presents challenges in accurately identifying structural variants.

Purpose of the Study:

  • To compare heuristic-based quality filtering and visual curation methods for structural variant calling.
  • To assess the impact of manual curation on the accuracy of structural variant datasets.
  • To establish a cost-effective strategy for generating high-confidence structural variant callsets from short-read data.

Main Methods:

  • Genome-wide structural variation landscape was characterized across 33 Nordic house sparrows (Passer domesticus).
  • Heuristic-based quality filtering and visual curation (Samplot/PlotCritic, Samplot-ML) were compared.
  • Manual curation strategies, including lenient and stringent approaches, were evaluated.

Main Results:

  • Manual curation significantly reduces false positive structural variants, with a lenient strategy removing up to 80%.
  • Variants rejected by manual curation showed no correlation with expected population structure from SNPs.
  • Variants passing curation reflected expected population structure, indicating higher confidence.
  • A lenient manual curation strategy by a single curator aligned with more stringent multi-curator assessments.

Conclusions:

  • Manual curation is vital for improving the reliability of structural variant callsets derived from short-read data.
  • Combining heuristic filtering with rapid manual curation offers a time- and cost-effective approach for population genomic studies.
  • This strategy enhances the proportion of high-confidence variants, crucial for downstream functional and population analyses.