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Related Concept Videos

Exon Recombination02:32

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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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In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
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Exon capture optimization in amphibians with large genomes.

Evan McCartney-Melstad1, Genevieve G Mount1,2,3, H Bradley Shaffer1

  • 1Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.

Molecular Ecology Resources
|May 26, 2016
PubMed
Summary

Optimizing target capture protocols by increasing repetitive sequence blockers and input DNA significantly improved genomic data efficiency for large-genome species. This enhancement doubles target capture efficiency, making genomic screening more affordable.

Keywords:
amphibianexon capturelarge genometarget enrichment

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genomic-scale data acquisition is difficult for nonmodel species with large, complex genomes.
  • Transcriptome sequencing offers a viable approach for these organisms, enabling the design of sequence capture probes for exonic regions.

Purpose of the Study:

  • To investigate modifications to standard protocols to enhance sequence capture efficiency in nonmodel organisms with large genomes.
  • To reduce sequencing costs through improved target enrichment efficiency.

Main Methods:

  • Conducted a replicated factorial experiment to test protocol modifications.
  • Manipulated amounts of Cot-1 repetitive sequence blocker and input DNA in target enrichment reactions.

Main Results:

  • Increased Cot-1 blocker and input DNA reduced PCR duplication rates.
  • This led to a near doubling of unique reads mapping to target sequences (from 10.4% to 19.9%).
  • Overall target capture efficiency was significantly improved.

Conclusions:

  • Modified target capture protocols can efficiently screen vertebrates, including amphibians, with large genomes.
  • The study demonstrates a more efficient and affordable method for genomic analysis in challenging taxa.