Limitations of Pseudogenes in Identifying Gene Losses

  • James C. Costello
  • Mira V. Han
  • Matthew W. Hahn
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)


The loss of previously established genes has been proposed as a major force in evolutionary change. While the sequencing of many new species offers the opportunity to identify cases of gene loss, the best method to do this with is unclear. A number of methods to identify gene losses rely on the presence of a pseudogene for each loss. If genes are completely or largely removed from the genome, however, such methods will fail to identify these cases. As the fate of gene losses is still unclear, we attempt to identify losses using nine Drosophila genomes and determine whether these lost genes leave behind pseudogenes in the lineage leading to D. melanogaster. We were able to find 109 cases of unambiguous gene loss. Of these, a maximum of 18 have identifiable pseudogenes, while the other 91 do not. We were also able to identify a large number of previously unannotated genes in the D. melanogaster genome, most of which also had evidence for transcription. Though our results suggest that pseudogene-based methods for finding gene losses will miss a large proportion of these events, we discuss the dependence of these conclusions on the divergence times among the species considered.


Genome Assembly Gene Loss Query Sequence Heterochromatic Region Drosophila Genome 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • James C. Costello
    • 1
    • 2
  • Mira V. Han
    • 1
    • 2
  • Matthew W. Hahn
    • 1
    • 2
  1. 1.School of InformaticsIndiana UniversityBloomingtonUSA
  2. 2.Department of BiologyIndiana UniversityBloomingtonUSA

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