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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 JBrowse, 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 5. Drosophila Polytene Chromosome Maps.
