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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
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Related Experiment Video

Updated: Feb 6, 2026

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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Assessing genome assembly quality using the LTR Assembly Index (LAI).

Shujun Ou1,2, Jinfeng Chen3, Ning Jiang1,2

  • 1Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.

Nucleic Acids Research
|August 15, 2018
PubMed
Summary

We developed a new metric, the LTR Assembly Index (LAI), to assess plant genome assembly quality, specifically focusing on long terminal repeat retrotransposons (LTR-RTs). LAI improves genome assembly evaluation and highlights the benefits of long-read sequencing technologies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Assembling plant genomes is difficult due to repetitive sequences, particularly long terminal repeat retrotransposons (LTR-RTs).
  • Existing methods lack a standard for evaluating the assembly of repeat regions in genomes.
  • Poorly assembled LTR-RTs impact the accuracy and completeness of draft genomes.

Purpose of the Study:

  • To introduce a novel, reference-free metric, the LTR Assembly Index (LAI), for evaluating genome assembly continuity.
  • To assess the effectiveness of LAI in quality control and improvement of genome assemblies.
  • To compare the impact of different sequencing technologies on genome assembly continuity using LAI.

Main Methods:

  • Developed the LTR Assembly Index (LAI) based on the analysis of LTR retrotransposons (LTR-RTs).
  • Corrected LAI for LTR-RT amplification dynamics to ensure independence from genome size and content.
  • Compared genome assemblies generated by short-read and long-read sequencing techniques.

Main Results:

  • LAI is a robust metric, independent of genome size, LTR-RT content, and gene space metrics (BUSCO, CEGMA).
  • Long-read sequencing technologies significantly improve genome assembly continuity compared to short-read methods.
  • LAI can guide iterative assembly refinement, assembler selection, and identification of low-quality genomic regions.

Conclusions:

  • The LTR Assembly Index (LAI) provides a standardized, reference-free method for evaluating plant genome assembly quality.
  • LAI demonstrates the superiority of long-read sequencing for achieving continuous genome assemblies.
  • The LAI tool is available to facilitate better genome assembly and analysis in genomics research.