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Related Concept Videos

Genome Annotation and Assembly03:36

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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Next-generation Sequencing

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Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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Related Experiment Video

Updated: May 18, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Next-generation phylogenomics using a Target Restricted Assembly Method.

Kevin P Johnson1, Kimberly K O Walden, Hugh M Robertson

  • 1Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA. kpjohnso@illinois.edu

Molecular Phylogenetics and Evolution
|September 25, 2012
PubMed
Summary
This summary is machine-generated.

The Target Restricted Assembly Method (TRAM) offers a cost-effective way to analyze phylogenetics using next-generation sequencing data. This technique bypasses full genome assembly, making genomic data more accessible for evolutionary studies.

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Last Updated: May 18, 2026

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Published on: January 25, 2019

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

  • Genomics
  • Phylogenetics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) provides vast amounts of genomic data cost-effectively.
  • Full genome assembly and annotation are time-consuming and labor-intensive, posing a challenge for phylogenetics.
  • Efficient methods are needed to leverage NGS data for phylogenetic analyses without extensive computational resources.

Purpose of the Study:

  • To introduce and validate the Target Restricted Assembly Method (TRAM) for phylogenetic data generation.
  • To demonstrate a cost-effective and feasible approach for utilizing NGS data in phylogenetics.
  • To bypass the need for complete genome assembly and annotation in phylogenetic studies.

Main Methods:

  • Protein sequences of target genes are used to query NGS data from related species via tblastn.
  • Identified gene fragments are assembled into contigs.
  • Contigs are aligned to reference cDNA sequences to remove introns, yielding protein-coding sequences.

Main Results:

  • The Target Restricted Assembly Method (TRAM) was successfully applied to 20 species of lice (Insecta: Psocodea).
  • A phylogenetic dataset comprising 10 nuclear protein-coding genes was generated.
  • The method proved effective in producing usable sequence data from genomic scale datasets.

Conclusions:

  • TRAM provides a practical and economical alternative for generating phylogenetic data from NGS datasets.
  • This method significantly reduces the time and labor associated with traditional genome assembly and annotation for phylogenetics.
  • The use of DNA over RNA offers advantages in cost-effectiveness and feasibility for phylogenetic analyses.