Conserved cluster organization of insect Runx genes

  • Riyue Bao
  • Markus FriedrichEmail author
Sequence Corner


Runx gene family transcription factors play important regulatory roles in metazoan development. The Drosophila genome contains four Runx genes, two of which are well studied (runt and lozenge) and two of which have not been explored in depth yet (CG42267 and CG34145). In the absence of paralog-specific orthologs in vertebrates, we investigated the evolutionary conservation of the Drosophila Runx genes in the genomes of mosquito, red flour beetle, honeybee, and distantly related Bilateria. All four Drosophila Runx genes are conserved in other endopterygote insects. Strikingly, their genetic linkage and genomic arrangement is also highly conserved despite past recombination events in the same genomic region. The preservation of Runx gene cluster organization for at least 300 million years resembles that of insect Hox and selected Wnt genes. We propose a model for the conserved cluster organization of developmental gene family paralogs based on differential coduplication of regulatory elements that act over long distances.


Developmental gene family evolution Synteny Gene cluster Wnt Hox Intron evolution 



We are grateful to Susan St.Pierre for prompt Flybase gene annotation correction, Jason Caravas for comments on the manuscript, and the two anonymous reviewers for stimulating suggestions. Riyue Bao was supported by a WSU College of Arts and Sciences Rumble Research Fellowship. Markus Friedrich was supported by a WSU Career Development Chair Award.

Supplementary material

427_2008_244_MOESM1_ESM.doc (99 kb)
Supplementary File 1 Multiple sequence alignment of Runx gene orthologs. (DOC 99.0 KB)
427_2008_244_MOESM2_ESM.doc (31 kb)
Supplementary File 2 142 amino acid site alignment of Runx domain in FASTA format. (DOC 31.0 KB)
427_2008_244_MOESM3_ESM.doc (126 kb)
Supplementary File 3 Runx gene tree reconstruction including the Caenorhabditis elegans Runx homolog rnt-1. (DOC 126 KB)
427_2008_244_MOESM4_ESM.xls (22 kb)
Supplementary File 4 Details of Runx gene annotation. (XLS 21.5 KB)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of Biological SciencesWayne State UniversityDetroitUSA
  2. 2.Department of Anatomy and Cell BiologyWayne State University, School of MedicineDetroitUSA

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