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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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Export of Mitochondrial and Chloroplast Genes02:19

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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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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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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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Related Experiment Video

Updated: Jul 4, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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Global exact optimisations for chloroplast structural haplotype scaffolding.

Victor Epain1, Rumen Andonov2

  • 1GenScale, Centre Inria de l'Université de Rennes, IRISA, 263 Avenue Général Leclerc, 35700, Rennes, France.

Algorithms for Molecular Biology : AMB
|February 6, 2024
PubMed
Summary

This study presents a new method for scaffolding chloroplast genomes by treating it as a discrete optimization problem. The approach prioritizes genomic repeats, enabling the identification of multiple genome forms within a single cell.

Keywords:
Genome assemblyInteger linear programmingInverted repeatsNP-complete problem

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Scaffolding is a critical step in genome assembly, involving the ordering and orientation of DNA contigs.
  • Existing scaffolding methods often rely on distance data, which may not fully exploit the unique characteristics of chloroplast genomes.
  • Chloroplast genomes are small, circular, and possess limited repeats, presenting specific challenges and opportunities for assembly.

Purpose of the Study:

  • To develop a novel scaffolding approach tailored for chloroplast genomes.
  • To address the limitations of existing methods by focusing on genomic region-specific features rather than inter-contig distances.
  • To accurately reconstruct complex chloroplast genomes, including multiple coexisting forms (haplotypes).

Main Methods:

  • Formulated chloroplast genome scaffolding as a discrete optimization problem, proving its decision version to be NP-Complete.
  • Incorporated biological knowledge of chloroplast genomes by defining mathematical constraints based on specific genomic repeats.
  • Developed an integer linear programming model implemented in the Python 3 package khloraascaf.
  • Utilized a genomic regions view, prioritizing the scaffolding of repeats.

Main Results:

  • The proposed method successfully models biological knowledge of genomic structures for chloroplast genome scaffolding.
  • The approach is independent of distance data and focuses on the relationships between specific genomic repeats.
  • The integer linear programming model effectively handles the structural haplotype issue, retrieving multiple genome forms.
  • Performance was evaluated on synthetic data, demonstrating robustness against various challenges.

Conclusions:

  • Biological knowledge of genomic structures can be effectively modeled to scaffold chloroplast genomes.
  • A genomic regions-based approach is sufficient for scaffolding repeats and identifying diverse genome forms.
  • The khloraascaf package provides a robust solution for complex chloroplast genome assembly challenges.