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SUPPLEMENTARY FIGURES
Supplementary Figure S1. Percentage of the assembled genome for each species that is
covered by synteny blocks (of greater than 1 gene) computed in comparison to the D.
melanogaster gene order. The size of each assembled genome is listed in Supplementary
Table S2.
Supplementary Figure S2: Gene trees based on SRP54 and SRP19 gene amino acid
sequences generated using PHYLIP (FELSENSTEIN 1989). (a) Using maximum likelihood.
(b) Using parsimony. Coding gene sequences were obtained from GLEAN-R
(DROSOPHILA 12 GENOMES CONSORTIUM 2007) gene predictions.
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SUPPLEMENTARY TABLES
Supplementary Table S1:
Species
D. sechellia
D. simulans
D. yakuba
D. erecta
D. ananassae
D. pseudoobscura
D. persimilis
D. willistoni
D. virilis
D. mojavensis
D. grimshawi
D. melanogaster orthology.
1:1 D. melanogaster
hi-confidence
orthologs w/o
collisions
12874
12658
12848
12787
12000
11653
11474
11489
11183
11100
10971
D. melanogaster
orthologs after Synpipe
collision resolution
13683
13517
13630
13643
13214
12905
12843
12822
12668
12589
12494
For each species, the number of D. melanogaster genes with an orthologous placement
are listed. These are based on synteny maximization and do not specify gene models or
complete coding extents. Collision resolution refines orthology data by including gene
clusters, nested genes, and by clearing up paralogous hits.
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Supplementary Table S2:
Synteny statistics for raw genome assembly (including
unmapped scaffolds).
Species
D. sechellia
D. simulans
D. yakuba
D. erecta
D. ananassae
D. pseudoobscura
D. persimilis
D. willistoni
D. virilis
D. mojavensis
D. grimshawi
Orthologs
#Synteny
Blocks
#genes
in syn
blocks
Max.
Syn.
Block
(#genes)
Avg.
Syn
Block
(#genes)
#Single
tons
13683
13517
13630
13643
13214
12905
12843
12822
12668
12589
12494
113
307
163
78
736
974
1016
1485
1336
1358
1408
13635
12849
13528
13616
12847
12348
12237
11911
11883
11773
11579
1768
1075
763
972
138
109
109
88
81
62
78
120.46
41.85
82.99
174.56
17.45
12.67
12.04
8.02
8.89
8.66
8.22
48
668
102
27
367
557
606
911
785
819
915
Assembled
Genome size
(bp)
166577145
137828247
168647858
152712140
230993012
152738921
188374079
236693122
206026697
193826310
200467819
For each species, synteny statistics compared to the D. melanogaster gene order, for the
complete genome assembly, are listed (including scaffolds that were not anchored to
chromosome arms). The number of orthologs is the same as in the post collisionresolution set shown in Table S1. The number and composition (number of genes,
maximum and average size in number of genes) vary in accordance with the phylogenetic
distribution of the genus Drosophila. The percentage of the genome assembly covered by
synteny blocks varies between 55-77%.
3
% genome
in synteny
blocks
68
77
71
77
55
76
60
58
62
68
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Supplementary Table S3.
Linkage chain analysis statistics: Genes, inversions,
breakpoints and re-usage index.
Muller Sp 1
Sp 2
Div
Genes Inv BP
r
%Chain(2)
A
D_mel
D_ana
Sophophora
1136
156 227 1.374
0.639
A
D_mel
D_pse
Sophophora
1136
194 246 1.577
0.519
A
D_mel
D_wil
Sophophora
1136
393 439 1.790* 0.696
A
D_mel
D_gri
Soph v Dros
1136
341 396 1.722* 0.655
A
D_mel
D_moj
Soph v Dros
1136
316 366 1.727* 0.720
A
D_mel
D_vir
Soph v Dros
1136
308 362 1.702
0.685
A
D_ana
D_pse
Sophophora
1136
205 261 1.571
0.536
A
D_ana
D_wil
Sophophora
1136
409 455 1.798* 0.717
A
D_ana
D_gri
Soph v Dros
1136
359 413 1.738* 0.648
A
D_ana
D_moj
Soph v Dros
1136
325 381 1.706* 0.554
A
D_ana
D_vir
Soph v Dros
1136
319 379 1.683
A
D_pse
D_wil
Sophophora
1136
390 442 1.765* 0.712
A
D_pse
D_gri
Soph v Dros
1136
325 369 1.762* 0.727
A
D_pse
D_moj
Soph v Dros
1136
299 347 1.723* 0.688
A
D_pse
D_vir
Soph v Dros
1136
288 343 1.679
A
D_wil
D_gri
Soph v Dros
1136
451 504 1.790* 0.736
A
D_wil
D_moj
Soph v Dros
1136
427 485 1.761* 0.759
A
D_wil
D_vir
Soph v Dros
1136
426 484 1.760* 0.724
A
D_gri
D_moj
Drosophila
1136
111 156 1.423
0.583
0.636
0.667
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A
D_gri
D_vir
Drosophila
1136
99
146 1.356
0.660
A
D_moj
D_vir
Drosophila
1136
42
68
1.235
0.769
B
D_mel
D_ana
Sophophora
1273
94
148 1.270
0.685
B
D_mel
D_pse
Sophophora
1273
111 169 1.314
0.655
B
D_mel
D_wil
Sophophora
1273
238 331 1.438
0.688
B
D_mel
D_gri
Soph v Dros
1273
187 250 1.496
0.635
B
D_mel
D_moj
Soph v Dros
1273
179 248 1.444
0.667
B
D_mel
D_vir
Soph v Dros
1273
179 244 1.467
0.708
B
D_ana
D_pse
Sophophora
1273
121 169 1.432
0.667
B
D_ana
D_wil
Sophophora
1273
244 326 1.497
0.659
B
D_ana
D_gri
Soph v Dros
1273
196 255 1.537
0.627
B
D_ana
D_moj
Soph v Dros
1273
184 247 1.490
0.635
B
D_ana
D_vir
Soph v Dros
1273
182 242 1.504
0.667
B
D_pse
D_wil
Sophophora
1273
233 309 1.508
0.632
B
D_pse
D_gri
Soph v Dros
1273
188 246 1.528
0.690
B
D_pse
D_moj
Soph v Dros
1273
170 234 1.453
0.641
B
D_pse
D_vir
Soph v Dros
1273
170 234 1.453
0.688
B
D_wil
D_gri
Soph v Dros
1273
261 334 1.563
0.619
B
D_wil
D_moj
Soph v Dros
1273
245 319 1.536
0.676
B
D_wil
D_vir
Soph v Dros
1273
240 318 1.509
0.705
B
D_gri
D_moj
Drosophila
1273
59
93
1.269
0.735
B
D_gri
D_vir
Drosophila
1273
57
87
1.310
0.767
B
D_moj
D_vir
Drosophila
1273
24
40
1.200
0.688
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C
D_mel
D_ana
Sophophora
1481
88
132 1.333
0.727
C
D_mel
D_pse
Sophophora
1481
159 230 1.383
0.535
C
D_mel
D_wil
Sophophora
1481
255 351 1.453
0.573
C
D_mel
D_gri
Soph v Dros
1481
217 301 1.442
0.571
C
D_mel
D_moj
Soph v Dros
1481
204 286 1.427
0.537
C
D_mel
D_vir
Soph v Dros
1481
203 281 1.445
0.526
C
D_ana
D_pse
Sophophora
1481
162 235 1.379
0.575
C
D_ana
D_wil
Sophophora
1481
265 359 1.476
0.596
C
D_ana
D_gri
Soph v Dros
1481
230 319 1.442
0.629
C
D_ana
D_moj
Soph v Dros
1481
219 312 1.404
0.634
C
D_ana
D_vir
Soph v Dros
1481
216 303 1.426
0.621
C
D_pse
D_wil
Sophophora
1481
284 387 1.468
0.631
C
D_pse
D_gri
Soph v Dros
1481
256 339 1.510
0.735
C
D_pse
D_moj
Soph v Dros
1481
245 331 1.480
0.698
C
D_pse
D_vir
Soph v Dros
1481
241 323 1.492
0.695
C
D_wil
D_gri
Soph v Dros
1481
288 392 1.469
0.635
C
D_wil
D_moj
Soph v Dros
1481
279 379 1.472
0.630
C
D_wil
D_vir
Soph v Dros
1481
275 378 1.455
0.621
C
D_gri
D_moj
Drosophila
1481
53
93
1.140* 0.825
C
D_gri
D_vir
Drosophila
1481
48
77
1.247
0.759
C
D_moj
D_vir
Drosophila
1481
37
62
1.194
0.833
D
D_mel
D_ana
Sophophora
1475
67
104 1.288
0.703
D
D_mel
D_pse
Sophophora
1475
122 176 1.386
0.685
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D
D_mel
D_wil
Sophophora
1475
266 361 1.474
0.642
D
D_mel
D_gri
Soph v Dros
1475
204 294 1.388
0.667
D
D_mel
D_moj
Soph v Dros
1475
182 260 1.400
0.667
D
D_mel
D_vir
Soph v Dros
1475
180 259 1.390
0.671
D
D_ana
D_pse
Sophophora
1475
128 183 1.399
0.745
D
D_ana
D_wil
Sophophora
1475
274 365 1.501
0.659
D
D_ana
D_gri
Soph v Dros
1475
209 296 1.412
0.678
D
D_ana
D_moj
Soph v Dros
1475
189 264 1.432
0.693
D
D_ana
D_vir
Soph v Dros
1475
187 263 1.422
0.684
D
D_pse
D_wil
Sophophora
1475
280 372 1.505
0.641
D
D_pse
D_gri
Soph v Dros
1475
210 303 1.386
0.717
D
D_pse
D_moj
Soph v Dros
1475
190 269 1.413
0.709
D
D_pse
D_vir
Soph v Dros
1475
188 270 1.393
0.707
D
D_wil
D_gri
Soph v Dros
1475
322 421 1.530
0.708
D
D_wil
D_moj
Soph v Dros
1475
302 398 1.518
0.615
D
D_wil
D_vir
Soph v Dros
1475
304 402 1.512
0.622
D
D_gri
D_moj
Drosophila
1475
38
69
1.101* 0.774
D
D_gri
D_vir
Drosophila
1475
38
71
1.070* 0.848
D
D_moj
D_vir
Drosophila
1475
10
19
1.053
E
D_mel
D_ana
Sophophora
1672
119 187 1.273* 0.706
E
D_mel
D_pse
Sophophora
1672
157 233 1.348
0.697
E
D_mel
D_wil
Sophophora
1672
274 354 1.548
0.738
E
D_mel
D_gri
Soph v Dros
1672
253 339 1.493
0.814
0.889
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E
D_mel
D_moj
Soph v Dros
1672
235 320 1.469
0.741
E
D_mel
D_vir
Soph v Dros
1672
234 319 1.467
0.729
E
D_ana
D_pse
Sophophora
1672
161 230 1.400
0.797
E
D_ana
D_wil
Sophophora
1672
278 357 1.557
0.734
E
D_ana
D_gri
Soph v Dros
1672
255 332 1.536
0.779
E
D_ana
D_moj
Soph v Dros
1672
236 314 1.503
0.731
E
D_ana
D_vir
Soph v Dros
1672
236 311 1.518
0.693
E
D_pse
D_wil
Sophophora
1672
272 351 1.550
0.646
E
D_pse
D_gri
Soph v Dros
1672
247 333 1.483
0.709
E
D_pse
D_moj
Soph v Dros
1672
233 314 1.484
0.667
E
D_pse
D_vir
Soph v Dros
1672
231 313 1.476
0.707
E
D_wil
D_gri
Soph v Dros
1672
318 407 1.563
0.708
E
D_wil
D_moj
Soph v Dros
1672
305 381 1.601
0.697
E
D_wil
D_vir
Soph v Dros
1672
300 386 1.554
0.744
E
D_gri
D_moj
Drosophila
1672
68
102 1.333
0.735
E
D_gri
D_vir
Drosophila
1672
64
94
1.362
0.667
E
D_moj
D_vir
Drosophila
1672
42
71
1.183
0.759
Species: D_mel, D. melanogaster; D_ana, D. ananassae; D_pse, D. pseudoobscura;
D_wil, D. willistoni; D_vir, D. virilis; D_moj, D. mojavensis; D_gri, D. grimshawi. Div,
indicates if the two species compared are within the Sophophora or Drosophila or
compared between the two genera; Genes, number of genes; Inv, number of inversions;
BP, number of breakpoints; r, re-usage index (SANKOFF and TRINH 2005); %Chain(2),
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percentage of linkage chains with 2 breakpoints. *, indicates a re-usage value less than or
greater than expected given a model of breakpoint hot spots.
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Supplementary Table S4:
Whole-genome rearrangement rates using ancestral gene
arrangement inference and micro-synteny breaks.
Species
D. melanogaster
D. sechellia
D. simulans
D. yakuba
D. erecta
D. ananassae
D. pseudoobscura
D. persimilis
D. willistoni
D. virilis
D. mojavensis
D. grimshawi
Rearrangement Rate Rearrangement Rate
with 62.9 MYA
with 39.2 MYA
(Tamura et al.)
(Russo et al.)
NGP Rearr divergence estimate divergence estimate
break count (Disruptions/Mb/MY) (Disruptions/Mb/MY)
603
0.08301
0.13320
648
0.08921
0.14314
*
770
0.10600
0.17009
622
0.08563
0.13740
722
0.09939
0.15949
628
0.08645
0.13872
619
0.08521
0.13673
*
297
0.04089
0.06561
343
0.04722
0.07577
496
0.06828
0.10956
Rearrangement break counts (from the root of the genus Drosophila tree) were
inferred using the NGP algorithm (BHUTKAR et al. 2007a). These rates are
comparable to slightly higher for the subgenus Sophophora species. They are
comparable to slightly lower for the subgenus Drosophila species, suggesting
lower number of rearrangements in this subgenus. D. melanogaster’s whole
genome size (~115Mb) was used. D. simulans (assembly quality) and D.
willistoni (ambiguity in phylogenetic partitioning – see Discussion) were
excluded from this analysis.
LIST OF SUPPLEMENTARY FILES



bhutkar_et_al_README.pdf
bhutkar_et_al_species_vs_dmel_synteny_report.xls
bhutkar_et_al_multi_species_conserved_blocks.xls
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