Background: A primary objective of comparative genomics is to identify genomic elements of functional
significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications,
rearrangements, translocations) may be widespread, and have important effects on organismal diversity. Any survey
of genomic variation is incomplete without an assessment of structural changes.
Results: We re-examine the genome sequences of the diverged species Drosophila melanogaster and D.
pseudoobscura to identify fine-scale structural features that distinguish the genomes. We detect 95 large insertion/
deletion events that occur within the introns of orthologous gene pairs, the majority of which represent insertion
of transposable elements. We also identify 143 microinversions below 5 kb in size. These microinversions reside
within introns or just upstream or downstream of genes, and invert conserved DNA sequence. The sequence
conservation within microinversions suggests they may be enriched for functional genetic elements, and their
position with respect to known genes implicates them in the regulation of gene expression. Although we found a
distinct pattern of GC content across microinversions, this was indistinguishable from the pattern observed across
blocks of conserved non-coding sequence.
Conclusion: Drosophila has long been known as a genus harboring a variety of large inversions that disrupt
chromosome colinearity. Here we demonstrate that microinversions, many of which are below 1 kb in length,
located in/near genes may also be an important source of genetic variation in Drosophila. Further examination of
other Drosophila genome sequences will likely identify an array of novel microinversion events.
Macdonald, S.J. and Long, A.D. Fine Scale Structural Variants Distinguish the Genomes of Drosophilia Melanogaster and D. Pseudoobscura. Genome Biology 2006, 7:R67. http://dx.doi.org/10.1186/gb-2006-7-7-r67