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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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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Molecular Evolution of the Tre Recombinase
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Recombination in Bacterial Genomes: Evolutionary Trends.

Anton E Shikov1,2, Iuliia A Savina1, Anton A Nizhnikov1,2

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|September 27, 2023
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Summary

Bacterial homologous recombination (HR) and horizontal gene transfer (HGT) drive adaptation and evolution. Analyzing genomic data reveals these genetic exchanges are linked to mobile genetic elements (MGEs) and impact bacterial lifestyles.

Keywords:
HGTHRecological adaptationhomologous recombinationhorizontal gene transferpathogenesissymbiosis

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Area of Science:

  • Microbial genomics
  • Evolutionary biology
  • Bacterial genetics

Background:

  • Homologous recombination (HR) and horizontal gene transfer (HGT) are key evolutionary processes in bacteria.
  • These genetic exchanges can influence bacterial fitness, specialization, speciation, and virulence.
  • Understanding the scope and genomic location of these events is crucial for deciphering bacterial adaptation.

Purpose of the Study:

  • To functionally characterize and determine the genomic context of recombination events in bacteria.
  • To analyze computational studies detecting recombination in bacterial genomes over the past 30 years.

Main Methods:

  • Systematic analysis of published genomic studies reporting recombination events.
  • Identification and categorization of genomic loci associated with DNA transfer.
  • Functional annotation of genes within mobile genetic elements (MGEs) involved in recombination.

Main Results:

  • Detected DNA transfer events were associated with mobile genetic elements (MGEs).
  • Genes within these MGEs encode proteins involved in diverse cellular functions, including secretion systems, toxins, and biosynthesis.
  • Recombination events were classified into three primary lifestyle categories: ecological diversification, pathogenesis, and symbiosis.

Conclusions:

  • Bacterial adaptation is significantly shaped by recombination-dependent mechanisms.
  • Symbiotic lifestyles appear to be particularly influenced by ancestral recombination events.
  • The study highlights the functional impact and genomic context of genetic exchange in bacterial evolution.