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Related Concept Videos

Synteny and Evolution02:31

Synteny and Evolution

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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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...
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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Setting up JBrowse 2 for Visualizing Genome Synteny.

Colin Diesh1, Garrett Stevens1, Scott Cain2

  • 1Department of Bioengineering, University of California, Berkeley, California.

Current Protocols
|December 5, 2025
PubMed
Summary
This summary is machine-generated.

This protocol details using JBrowse 2, an open-source genome browser, to visualize genomic synteny. It guides users through data preparation and setup for exploring conserved sequences across multiple genomes.

Keywords:
comparative genomicsdata visualizationgenome browsersyntenywhole‐genome alignment

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome browsers are essential tools for visualizing genomic data.
  • Understanding syntenic relationships aids in comparative genomics and evolutionary studies.
  • JBrowse 2 offers advanced features for multi-genome visualization.

Purpose of the Study:

  • To provide a protocol for setting up synteny views in JBrowse 2.
  • To demonstrate the visualization of whole-genome alignments for synteny analysis.
  • To facilitate the exploration of conserved sequences across multiple genomes.

Main Methods:

  • Data preparation for whole-genome alignment (WGA) data.
  • Formatting WGA data into JBrowse 2 compatible formats.
  • Utilizing JBrowse 2's graphical user interface (GUI) for interactive synteny view setup.

Main Results:

  • Successful generation of synteny views in JBrowse 2.
  • Creation of publication-quality figures from synteny visualizations.
  • Demonstration of JBrowse 2's capability for comparative genomics.

Conclusions:

  • JBrowse 2 provides an effective platform for visualizing genomic synteny.
  • The described protocol simplifies the process of comparative genome analysis.
  • This method enhances the exploration of conserved genomic regions across species.