61500
270500
272500
400
300
200
737000
100
0
60500
61000
61500
271500
50
0
60500
61000
300
200
100
61500
271500
500
0
200
100
0
60000
60500
61000
61500
271500
100
50
0
400
300
200
100
0
60500
61000
61500
737500
738000
271500
272500
804000
4000
2000
804000
200
737500
738000
738500
1211500
1000
100
50
933500
200
100
50
934500
1211500
804000
805000
1212000
350
300
250
200
150
100
50
0
1212500
100
50
933500
934500
1232000
1231000
1231500
1232000
1231000
1231500
1232000
1231500
1232000
1231500
1232000
adult male 5 days
150
100
50
0
932500
1231500
1231000
adult male 5 days
250
150
1231000
adult female 5 days
0
932500
0
803000
350
300
250
200
150
100
50
0
1212500
150
adult male 5 days
2000
1212000
adult female 5 days
200
1232000
WPP 3 days
250
250
3000
350
300
250
200
150
100
50
0
1212500
50
934500
150
805000
0
737000
933500
0
803000
1212000
150
100
0
932500
adult male 5 days
100
1211500
200
adult female 5 days
5000
200
50
WPP 3 days
50
1231500
L1 larvae
250
250
1000
350
300
250
200
150
100
50
0
1212500
100
934500
150
200
1212000
200
150
0
933500
100
805000
3000
738500
1211500
0
803000
350
300
250
200
150
100
50
0
L1 larvae
932500
0
737000
0
270500
1000
adult male 5 days
50
250
200
adult female 5 days
300
100
WPP 3 days
5000
100
150
934500
250
3000
4000
933500
50
805000
2000
738500
400
RNA−seq depth
150
738000
200
272500
804000
0
737500
300
adult male 5 days
600
60000
100
0
270500
adult male 5 days
250
932500
100
0
803000
4000
1231000
embryos 0−2 hours
200
L1 larvae
200
150
WD1292
WD1291
1212500
0
805000
1000
adult female 5 days
400
50
WPP 3 days
400
300
804000
5000
737000
100
250
738500
200
272500
RNA−seq depth
50
RNA−seq depth
100
738000
0
270500
RNA−seq depth
150
737500
300
adult female 5 days
600
500
803000
2000
0
737000
150
L1 larvae
4000
1212000
250
200
0
3000
WPP 3 days
0
60000
1000
5000
400
500
400
adult female 5 days
250
2000
738500
100
272500
RNA−seq depth
RNA−seq depth
150
738000
200
WPP 3 days
600
100
737500
300
0
270500
WPP 3 days
200
3000
L1 larvae
500
250
4000
0
400
RNA−seq depth
RNA−seq depth
RNA−seq depth
50
0
RNA−seq depth
271500
L1 larvae
250
RNA−seq depth
0
600
60000
100
1211500
embryos 0−2 hours
RNA−seq depth
61000
200
934500
RNA−seq depth
60500
5000
300
933500
embryos 0−2 hours
RNA−seq depth
60000
100
932500
WD1290
WD1289
RNA−seq depth
100
805000
WD1288−WD1290
WD1288
WD1287
RNA−seq depth
200
804000
RNA−seq depth
400
300
L1 larvae
200
150
803000
embryos 0−2 hours
400
500
0
250
738500
Wolbachia gene models
WD1271
WD1269
WD1268
RNA−seq depth
0
738000
WD1269−WD1270
WD1270
WD0976
WD0975
RNA−seq depth
50
737500
RNA−seq depth
100
RNA−seq depth
737000
embryos 0−2 hours
RNA−seq depth
150
200
272500
600
RNA−seq depth
RNA−seq depth
250
200
200
271500
RNA−seq depth
270500
embryos 0−2 hours
Wolbachia gene models
WD0974
WD0973
WD0972
WD0971
RNA−seq depth
61500
RNA−seq depth
61000
WD0973−WD0975
Wolbachia gene models
WD0838
RNA−seq depth
60500
WD0837−WD0838
WD0837
WD0836
WD0835
RNA−seq depth
60000
embryos 0−2 hours
Wolbachia gene models
WD0765
WD0764
RNA−seq depth
WD0763−WD0764
WD0763
WD0762
RNA−seq depth
Wolbachia gene models
WD0293
WD0292
RNA−seq depth
WD0291−WD0292
WD0291
WD0290
RNA−seq depth
Wolbachia gene models
WD0062
RNA−seq depth
WD0061−WD0062
WD0061
RNA−seq depth
Wolbachia gene models
1211500
1212000
1212500
1231000
Figure S4. Wolbachia genes with sex-biased expression are often found in operons.
Wiggle plots of Wolbachia expression levels for seven clusters of Wolbachia genes with sexbiased expression. Gene models and RNA-seq coverage for each stage are shown for the
forward and reverse strands in blue and red, respectively. RNA-seq plots are shown on the
same absolute y-axis scale. To provide an internal normalization factor for comparison across
samples, mean coverage of the stably-expressed Wsp/WD1063 gene (not shown in this interval) divided by twenty is depicted by the dashed line in each panel. Six out of seven
clusters (WD0061–WD0062, WD0291–WD0292, WD0837–WD0838, WD0973–WD0975,
WD1269–WD1270 and WD1288–WD1290) were confirmed as operons based on contiguous
mapping of RNA-seq reads. The third cluster depicted contains two divergently transcribed
genes (WD0763–WD0764) that are not co-transcribed as an operon.
8 SI
F. Gutzwiller et al.