Conserved cluster organization of insect Runx genes

Development Genes and Evolution

Volumn 218, Issue 10, 2008, Pages 567-574

  Bao, Riyue ^a   Friedrich, Markus ^a,b  

^a WAYNE STATE UNIVERSITY   (United States)

^b WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Developmental gene family evolution; Gene cluster; Hox; Intron evolution; Synteny; Wnt

Indexed keywords

DROSOPHILA PROTEIN; HOX PROTEIN; INSECT PROTEIN; TRANSCRIPTION FACTOR RUNX; WNT PROTEIN;

ARTICLE; BEETLE; CONTROLLED STUDY; DROSOPHILA; GENE CLUSTER; GENE DUPLICATION; GENETIC CONSERVATION; GENETIC LINKAGE; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC REGULATION; GENOME ANALYSIS; HONEYBEE; INSECT GENETICS; MOSQUITO; NONHUMAN; PARALOGY; PRIORITY JOURNAL;

ANIMALS; CONSERVED SEQUENCE; CORE BINDING FACTOR ALPHA SUBUNITS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE REARRANGEMENT; GENES, DEVELOPMENTAL; GENES, INSECT; HOMEODOMAIN PROTEINS; INTRONS; LINKAGE (GENETICS); MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID;

APIS MELLIFERA; BILATERIA; HEXAPODA; METAZOA; TRIBOLIUM CASTANEUM; VERTEBRATA;

EID: 54049119165     PISSN: 0949944X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00427-008-0244-x     Document Type: Article

References (42)

1. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Bae SC, Lee J (2000) cDNA cloning of run, a Caenorhabditis elegans Runt domain encoding gene. Gene 241:255-258
3. Bataille L et al (2005) Resolving embryonic blood cell fate choice in Drosophila: Interplay of GCM and RUNX factors. Development 132:4635-4644
4. Bolognesi R et al (2008) Tribolium Wnts: Evidence for a larger repertoire in insects with overlapping expression patterns that suggest multiple redundant functions in embryogenesis. Dev Genes Evol 218:193-202
5. Bolshakov VN et al (2002) A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. Genome Res 12:57-66
6. Boutros M et al (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303:832-835
7. Brown SJ et al (2002) Sequence of the Tribolium castaneum homeotic complex: The region corresponding to the Drosophila melanogaster antennapedia complex. Genetics 160:1067-1074
8. Choe CP et al (2006) A pair-rule gene circuit defines segments sequentially in the short-germ insect Tribolium castaneum. Proc Natl Acad Sci U S A 103:6560-6564
9. Coffman JA (2003) Runx transcription factors and the developmental balance between cell proliferation and differentiation. Cell Biol Int 27:315-324
10. Daga A et al (1996) Patterning of cells in the Drosophila eye by Lozenge, which shares homologous domains with AML1. Genes Dev 10:1194-1205
11. Dearden PK et al (2006) Patterns of conservation and change in honeybee developmental genes. Genome Res 16:1376-1384
12. Drysdale RA, Crosby MA (2005) FlyBase: Genes and gene models. Nucleic Acids Res 33:D390-D395
13. Duffy JB et al (1991) Expression and function of the Drosophila gene runt in early stages of neural development. Development 113:1223-1230
14. Engstrom PG et al (2007) Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 17:1898-1908
15. Felsenstein J (1986) Jackknife, bootstrap and other resampling methods in regression analysis discussion. Ann Stat 14:1304-1305
16. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
17. Garcia-Fernandez J (2005) The genesis and evolution of homeobox gene clusters. Nat Rev Genet 6:881-892
18. Gergen JP, Butler BA (1988) Isolation of the Drosophila segmentation gene runt and analysis of its expression during embryogenesis. Genes Dev 2:1179-1193
19. Gergen JP, Wieschaus EF (1985) The localized requirements for a gene affecting segmentation in Drosophila: Analysis of larvae mosaic for runt. Dev Biol 109:321-335
20. Gupta BP, Rodrigues V (1995) Distinct mechanisms of action of the Lozenge locus in Drosophila eye and antennal development are suggested by the analysis of dominant enhancers. J Neurogenet 10:137-151
21. Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:931-949
22. Jones DT et al (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
23. Kagoshima H et al (1993) The Runt domain identifies a new family of heteromeric transcriptional regulators. Trends Genet 9:338-341
24. Kmita M, Duboule D (2003) Organizing axes in time and space; 25 years of colinear tinkering. Science 301:331-333
25. Lewis EB et al (2003) Evolution of the homeobox complex in the Diptera. Curr Biol 13:R587-R588
26. Negre B, Ruiz A (2007) HOM-C evolution in Drosophila: Is there a need for Hox gene clustering. Trends Genet 23:55-59
27. Putnam NH et al (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:86-94
28. Rennert J et al (2003) The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms. BMC Evol Biol 3:4
29. Robertson AJ et al (2002) The expression of SpRunt during sea urchin embryogenesis. Mech Dev 117:327-330
30. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
31. Savard J et al (2006) Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of holometabolous insects. Genome Res 16:1334-1338
32. Schmidt HA et al (2002) TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504
33. Severson DW et al (2004) Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae. J Hered 95:103-113
34. Shippy TD et al (2008) Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Dev Genes Evol 218:127-139
35. Stricker S et al (2003) A single amphioxus and sea urchin runt-gene suggests that runt-gene duplications occurred in early chordate evolution. Dev Comp Immunol 27:673-684
36. Tamura K et al (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599
37. Thompson JD et al (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
38. Torres M, Sanchez L (1992) The segmentation gene runt is needed to activate Sex-lethal, a gene that controls sex determination and dosage compensation in Drosophila. Genet Res 59:189-198
39. Tribolium Genome Sequencing Consortium (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452:949-955
40. Waterhouse RM et al (2008) The Aedes aegypti genome: A comparative perspective. Insect Mol Biol 17:1-8
41. Zdobnov EM, Bork P (2007) Quantification of insect genome divergence. Trends Genet 23:16-20
42. Zdobnov EM et al (2002) Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298:149-159