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Genetic, Cytological and Genomic Map Coordinates for D. melanogaster Genes

FlyBase offers a downloadable spreadsheet that includes a cytogenetic-genetic-sequence location correspondence table, and listings of the genomic coordinates, cytological (polytene band) position and genetic map position for all annotated D. melanogaster genes (last updated June 15, 2016). Information for each chromosome arm is available on a separate tab of the spreadsheet. For genetic map positions we report experimentally determined values reported in the literature, the FlyBase computational estimate and an alternative computational estimate based on the mapping of millions of SNPs from thousands or recombination events Comeron et. al., 2012. Note that some heterochromatic regions of the Release 6 genome assembly were beyond the original scope of the FlyBase computation; for genes in these regions, values have been manually extrapolated to the end of the genome assembly (values shaded in gray).

D. melanogaster Chromosome Maps

Table 1. The original illustrations of D. melanogaster polytene chromosomes by Bridges and Slizynski.

Species Chromosome Muller Element References File
D. melanogaster X A Bridges 1938, Bridges 1935 Dmel_X_Bridges.png
D. melanogaster 2L B Bridges 1942, Bridges 1935 Dmel_2L_Bridges.png
D. melanogaster 2R C Bridges and Bridges 1939, Bridges 1935 Dmel_2R_Bridges.png
D. melanogaster 3L D Bridges 1941, Bridges 1935 Dmel_3L_Bridges.png
D. melanogaster 3R E Bridges 1941, Bridges 1935 Dmel_3R_Bridges.png
D. melanogaster 4 F Slizynski 1944 Dmel_4_Slizynski.png


Table 2. The original electron micrographs of D. melanogaster polytene chromosomes by Lefevre. These electron micrographs offer an alternative reference for checking polytene band references.

Species Chromosome Muller Element References File
D. melanogaster X A Lefevre 1976 Dmel_X_Lefevre.png
D. melanogaster 2L B Lefevre 1976 Dmel_2L_Lefevre.png
D. melanogaster 2R C Lefevre 1976 Dmel_2R_Lefevre.png
D. melanogaster 3L D Lefevre 1976 Dmel_3L_Lefevre.png
D. melanogaster 3R E Lefevre 1976 Dmel_3R_Lefevre.png
D. melanogaster 4 F Lefevre 1976 Dmel_4_Lefevre.png


Table 3. Electron micrograph maps of Drosophila melanogaster polytene chromosomes (Anja O. Saura, Asko J. Saura and Veikko Sorsa ). Electron micrograph (EM) maps of the polytene salivary gland chromosomes of D. melanogaster were published piecemeal in 1979-2002 mainly in the journal Hereditas (see references). Hereditas, Springer-Verlag and Georg Thieme Verlag granted permission to the authors to republish these maps on the web. Due to the retirement of the original authors the maps were removed from internet view. The authors have subsequently authorized FlyBase to make the maps available again. The EM maps can be used as an additional reference to check the locations of subdivision boundaries or the names of individual bands of a chromosome region in addition to the drawings of Bridges and the photographic maps of Lefevre.

Chromosome Arm References (by section) EM Image (by section)
X 1-2, 3-5, 6-10, 11-20 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
2L 21-22, 23-26, 27-29, 30-31, 32-36, 37-39 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
2R 41-50, 51-60 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
3L 61-63, 64-70, 71-73, 74-80 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
3R 81-90, 91-100 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
4 101-102 101
Chromocenter 101-102 102


Table 4. Annotated D. melanogaster chromosome maps that combine illustrations and electron micrographs with annotation of the genomic, genetic and cytological positions indicated for select genes. Note that for the Y chromosome, the micrograph shown is of a prometaphase mitotic chromosome. Note also that large genome assembly gaps are not depicted in GBrowse, and so Y chromosome genes look closer together than they really are. These images are also available on the FlyBase Chromosome Maps browser.

Species Chromosome Muller Element References File
D. melanogaster X A Dmel_X.png
D. melanogaster 2L B Dmel_2L.png
D. melanogaster 2R C Dmel_2R.png
D. melanogaster 3L D Dmel_3L.png
D. melanogaster 3R E Dmel_3R.png
D. melanogaster 4 F Dmel_4.png
D. melanogaster Y Kennison 1981, Hazelrigg et al., 1982, Gatti and Pimpinelli 1983 Dmel_Y.jpg
D. melanogaster M* Dmel_M.png
  • Note - the map provided for the mitochondrial genome assembly corresponds to the non-current, Release 5-associated accession U37541.1. For the current Release 6-associated mitochondrial genome assembly sequence, see accession NC_024511.2

Drosophila Chromosome Maps

The table below lists chromosome map images available for various non-melanogaster Drosophila species. Micrographs are from Schaeffer et al., 2008. Related chromosomes in different Drosophila species may have different names and even a different organization. As such, we list the Muller element correspondence for each chromosome arm, which represents the common chromosome arms among Drosophila species: A, B, C, D, E and F. These relationships are depicted in this Muller Element Arm Synteny Table, which also incorporates a view of the phylogenetic relationships of the species, their standard chromosomal numbering and the corresponding Muller element.

Take note:

  • There is not a simple one-to-one correspondence for all of the species chromosome arms and a single Muller element.
  • Species-specific chromosome images are not available for species closely related to D. melanogaster (D. simulans, D. sechellia, D. erecta and D. yakuba) - instead, schematic depictions of chromosomes in these species are shown next to images for homologous D. melanogaster chromosomes (with inversions relative to the D. melanogaster chromosome indicated).
  • For the D. mojavensis third chromosome (Muller element B) image, the micrograph (bottom) and drawing (center) do not fully correspond to each other. The micrograph is from the sequenced Santa Catalina strain that is homozygous for the f2=MU inversion. The drawing is taken from Ruiz et al., 1990, which is from a strain that does not have this inversion. See Delprat et al., 2014 for details.

Table 4. Drosophila Polytene Chromosome Maps.

Species Muller Element A Muller Element B Muller Element C Muller Element D Muller Element D Muller Element F
D. simulans Dsim_A_X.png Dsim_B_2L.png Dsim_C_2R.png Dsim_D_3L.png Dsim_E_3R.png Dsim_F_4.png
D. sechellia Dsec_A_X.png Dsec_B_2L.png Dsec_C_2R.png Dsec_D_3L.png Dsec_E_3R.png Dsec_F_4.png
D. yakuba Dyak_A_X.png Dyak_B-C_2L-2R.png Dyak_B-C_2L-2R.png Dyak_D_3L.png Dyak_E_3R.png Dyak_F_4.png
D. erecta Dere_A_X.png Dere_B-C_2L-2R.png Dere_B-C_2L-2R.png Dere_D_3L.png Dere_E_3R.png Dere_F_4.png
D. ananassae Dana_A_XL-XR.png Dana_B_2L.png Dana_C_2R.png Dana_D_3L.png Dana_E_3R.png
D. pseudoobscura Dpse_A_XL.png Dpse_B_4.png Dpse_C_3.png Dpse_D_XR.png Dpse_E_2.png Dpse_F_5.png
D. persimilis Dper_A_XL.png Dper_B_4.png Dper_C_3.png Dper_D_XR.png Dper_E_2.png Dper_F_5.png
D. willistoni Dwil_A_XL.png Dwil_B_2R.png Dwil_C_2L.png Dwil_D_XR.png Dwil_E-F_3.png Dwil_E-F_3.png
D. mojavensis Dmoj_A_X.png Dmoj_B_3.png Dmoj_C_5.png Dmoj_D_4.png Dmoj_E_2.png
D. virilis Dvir_A_X.png Dvir_B_4.png Dvir_C_5.png Dvir_D_3.png Dvir_E_2.png Dvir_F_6.png
D. grimshawi Dgri_A_X.png Dgri_B_3.png Dgri_C_2.png Dgri_D_5.png Dgri_E_4.png Dgri_F_6.png