Remodelling of a homeobox gene cluster by multiple independent gene reunions in Drosophila.
Genome clustering of homeobox genes is often thought to reflect arrangements of tandem gene duplicates maintained by advantageous coordinated gene regulation. Here we analyse the chromosomal organization of the NK homeobox genes, presumed to be part of a single cluster in the Bilaterian ancestor, across 20 arthropods. We find that the ProtoNK cluster was extensively fragmented in some lineages, showing that NK clustering in Drosophila species does not reflect selectively maintained gene arrangements. More importantly, the arrangement of NK and neighbouring genes across the phylogeny supports that, in two instances within the Drosophila genus, some cluster remnants became reunited via large-scale chromosomal rearrangements. Simulated scenarios of chromosome evolution indicate that these reunion events are unlikely unless the genome neighbourhoods harbouring the participating genes tend to colocalize in the nucleus. Our results underscore how mechanisms other than tandem gene duplication can result in paralogous gene clustering during genome evolution.
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Carolus
C
Chan
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Suvini
S
Jayasekera
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Bryant
B
Kao
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Moisés
M
Páramo
1] Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.
Marcin
M
von Grotthuss
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
José M
JM
Ranz
D000595:Amino Acid Sequence; D000818:Animals; D001181:Arthropods / Q000235:genetics; D002874:Chromosome Mapping; D019295:Computational Biology; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics*; D005801:Genes, Homeobox / Q000235:genetics*; D017403:In Situ Hybridization; D016013:Likelihood Functions; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D013045:Species Specificity; D014178:Translocation, Genetic / Q000235:genetics / Q000502:physiology*