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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. anannassae	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