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Related Concept Videos

The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
DNA-only Transposons02:57

DNA-only Transposons

DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
Chromosome Structure02:40

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

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Related Experiment Video

Updated: Jun 9, 2026

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

The repeatome landscape in the "Saccharum complex".

Nina Reis Soares1, Zirlane Portugal da Costa1, Luiz Augusto Cauz-Santos2

  • 1Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil.

Frontiers in Plant Science
|June 8, 2026
PubMed
Summary

The Saccharum repeatome shows shared ancestry and lineage-specific diversification, with repetitive DNA driving genome expansion and species differentiation in sugarcane. This research provides key genomic resources for understanding polyploid evolution.

Keywords:
RepeatExplorer2phylogenypolyploidrepetitive DNAsugarcane

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Last Updated: Jun 9, 2026

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
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Published on: August 12, 2019

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Area of Science:

  • Genomics
  • Plant Biology
  • Evolutionary Biology

Background:

  • The Saccharum complex includes genera that hybridize with Saccharum, contributing to modern sugarcane's complex genome.
  • Sugarcane's genome is characterized by polyploidy, rearrangements, and a large fraction of repetitive DNA.
  • The evolutionary dynamics of repetitive DNA across the Saccharum complex remain largely unexplored.

Purpose of the Study:

  • To analyze the repetitive DNA landscape across diverse Saccharum species and related genera.
  • To investigate the evolutionary dynamics and distribution of repetitive sequences, particularly LTR retrotransposons.
  • To understand the role of repetitive DNA in genome size variation and species differentiation within the Saccharum complex.

Main Methods:

  • Analysis of repetitive sequences in 30 genotypes from nine Saccharum species, sugarcane cultivars, and related genera using RepeatExplorer2.
  • Comparative clustering, correlation analyses, and repeat-based phylogenetic reconstruction to assess repeat lineage evolution.
  • Examination of LTR retrotransposons in assembled genomes of S. officinarum, S. spontaneum, and cultivar R570 using DANTE.

Main Results:

  • Repetitive DNA content varied from 42.5% to 59.7%, dominated by LTR retrotransposons (LTR-RTs).
  • Ty3 (Tekay) and Ty1 (SIRE) LTR-RTs showed significant interspecific variation, while satellite DNAs were taxon-specific.
  • Repeat abundance correlated strongly with genome size, indicating a role in genome expansion; repeat-based phylogenies largely supported existing Saccharum phylogenies.

Conclusions:

  • The Saccharum repeatome reflects both shared ancestry and significant lineage-specific diversification.
  • Repetitive DNA has been crucial for genome expansion and retains signatures of species differentiation and hybridization.
  • Identified repeat families offer valuable genomic resources for understanding polyploid genome dynamics in sugarcane.