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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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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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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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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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Widespread false gene gains caused by duplication errors in genome assemblies.

Byung June Ko1, Chul Lee2, Juwan Kim2

  • 1Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

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|September 27, 2022
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Summary

False duplications in genome assemblies inflate gene counts, leading to inaccurate biological findings. Advanced assembly methods are crucial for accurate gene family analysis and reliable genomic research.

Keywords:
Assembly errorDe novo assemblyFalse duplicationPhasing errorVertebrate genome project

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • False duplications in genome assemblies can lead to erroneous biological conclusions.
  • Previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird were analyzed for false duplications.
  • The Vertebrate Genomes Project (VGP) pipeline aims to eliminate false duplications via haplotype phasing and purging.

Purpose of the Study:

  • To quantify false duplications in previous and new genome assemblies.
  • To identify the sources and prevalence of false duplications.
  • To assess the effectiveness of VGP assembly methods in reducing false duplications.

Main Methods:

  • Whole genome alignments were performed to compare previous and VGP assemblies.
  • Analysis focused on identifying falsely duplicated sequences and their impact on gene counts.
  • Specific gene families, such as ancient ATP nucleotide binding genes, were examined for higher prevalence of false duplications.

Main Results:

  • Previous assemblies contained 4-16% falsely duplicated sequences, impacting numerous genes and leading to overestimated gene family expansions.
  • Heterotype duplications, where divergent haplotypes are misclassified, were the primary source of false duplications.
  • While VGP assemblies showed improvement, some false duplications persist and require purging.

Conclusions:

  • Advanced genome assembly methods are needed to better separate haplotypes and sequence errors.
  • Researchers should exercise caution when analyzing gene gains, especially in light of potential assembly artifacts.
  • Continuous refinement of genome assembly pipelines is essential for accurate genomic studies.