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Related Concept Videos

Synteny and Evolution02:31

Synteny and Evolution

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 Annotation and Assembly

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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Evolutionary Relationships through Genome Comparisons

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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Cis-regulatory Sequences

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...
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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...

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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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Published on: December 13, 2024

r2cat: synteny plots and comparative assembly.

Peter Husemann1, Jens Stoye

  • 1Genome Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany. peter.husemann@cebitec.uni-bielefeld.de

Bioinformatics (Oxford, England)
|December 18, 2009
PubMed
Summary
This summary is machine-generated.

Investigating closely related microbial strains is now feasible with advanced sequencing technologies. A new tool, r2cat, aids in comparative genome assembly and synteny analysis, overcoming challenges in genome finishing.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Advances in parallel pyrosequencing and genome sequencing projects facilitate the study of closely related microbial strains.
  • Genome finishing remains a significant challenge, often resulting in fragmented assemblies (contigs) rather than complete genomic sequences.

Purpose of the Study:

  • To introduce r2cat (related reference contig arrangement tool), a novel software for comparative genome assembly.
  • To provide a tool that assists in analyzing and visualizing synteny between related genomes.

Main Methods:

  • Development of the r2cat software for comparative assembly.
  • Implementation of interactive visualization features for synteny inspection.

Main Results:

  • r2cat facilitates the arrangement of contigs from newly sequenced strains against a reference genome.
  • The tool enables visual inspection of genomic synteny, aiding in the identification of rearrangements and conserved regions.

Conclusions:

  • r2cat addresses the challenge of genome finishing by enabling efficient comparative assembly of related strains.
  • The tool enhances the investigation of genomic structures and evolutionary relationships through interactive synteny visualization.