Chapter 2. Toxicity of the photosynthetic prey to unicellular predators under
3.5. Figures and tables
N : Naegleria sp. 19,827 A : Acanthamoeba sp. 20,264 V : Vannella sp. 15,302
A N. of total contigs
Down VA
N
5.0 2.5
0.0 V AN
Up
Percent contigs
>2 fold change (+Green) Specific to “Green”
(change less in “Pale” and “w/o prey” )
B
Dark Light
Glutathione peroxidase
1000
0 500
1000 500
0 500
1000 500
0 500
1000 500
N
593
253
859
441 993
587 1000
0 500
500 1292
505 1000
1000
1000
800
0 400
1000
0 500
800
400 500
0 400
800 400
0 400
800 400
1000
0 500
1000 500
A V
678311270547
17255235488147
0 400
1000
0 500
800
400 500
892123
6412621
COX15 Myosin type II
D
FPKM
400
0 200
100
0 50
400 200
400
0 200
400 200
400
0 200
400 200
100 50
100
0 50
100 50
N A
V
239616
14681773
14981719419125
400
0 200
100
0 50
400 200
100 50
5106
11131 2542319153
500
0 250
500 250
0 250
500 250
0 250
500 250 500
0 250
250
Green (rep. 2)w/o preyPaleGreen (rep. 1)
Green (rep. 2)w/o preyPaleGreen (rep. 1)
Light
Dark Light
Dark Light
Dark Light
Dark
200
0 100
300
0 150
100
0 50
200 100
300 150
100 50
0 100
200 100
0 100
200 100
0 150
300 150
0 150
300 150
100
0 50
100 50
N A
V
7712611783
54256131115134228
27
66 149
188 227
204 200
0 100
0 150
100
0 50
200 100
300 150
100 50
47104
38203
14
Green (rep. 2)w/o preyPaleGreen (rep. 1) 154
200 200
0 100
200 100
0 100
200 100
0 100
200 100
N
401154110450204
0 100
100
99110
ChlH2O2 (dark)RBw/o chl
w/
w/o Contig
Up 510
Chl U RB U H2O2 = 477 Down 556 Chl U RB U H2O2 = 474 Naegleria sp.+Green
Dark Light
194Chl 425RB
H2O2 368
269Chl
H2O2 RB 333
301
Figure 3.1. Effects of the photosynthetic traits of bacterial prey, chlorophyll, and ROS on transcriptome in Naegleria sp., Acanthamoeba sp. and Vannella sp.
Respective amoebae were co-cultured with green or pale S. elongatus or E. coli with or
N A V N A V Categories N A V Categories
Oxidaive stress responses V-ATPase Actomyosin
Carotene Respiration Motion
DNA repair Phagocytosis
Proteolysis Cytoskeleton
C
DownUp
Categories
without chlorophyll a under dark for 12 h (dark) and then transferred to light
(200 μE m-2 s-1) for 1 h (light). To examine the effect of illumination that is independent of prey, respective amoebae were cultured in an organic growth medium without prey under dark for 12 h (dark) and then transferred to light for 1 h (light). To examine the effects of singlet oxygen, Naegleria sp. was cultured without prey and with 30 nM Rose Bengal (RB), which produces singlet oxygen by illumination, under dark for 12 h (dark) was transferred to light for 1 h (light). To examine the effects of H2O2, Naegleria sp. was cultured without prey for 12 h under dark (w/o H2O2) was treated with 4 μM H2O2 under dark for 1 h (w/ H2O2). (A) Percentage of up (orange and red bars)/down-regulated (light blue and blue bars) (≥2-fold change) contigs when amoebae feeding on green under dark were transferred to light. The results shown are based on reproduction in two independent cultures and experiments (rep. 1 and rep. 2). Red and blue bars indicate contigs in which the magnitude of change upon illumination was compromised (the light/dark ration became less than the half of amoebae feeding on green S. elongatus) when feeding on pale S. elongatus or without prey. Thus changes in these contigs upon illumination are caused by photosynthetic trait of the green S. elongatus prey. (B) Area-weighted Venn diagrams showing the contents of up/down-regulated contigs in Naegleria sp. feeding on green S. elongatus upon illumination that are shared with Chl., RB, or H2O2.
Up/down-regulation in RB indicates contigs that exhibited ≥2-fold change in the presence of 30 nM RB only under illumination. Up/down-regulation in H2O2 indicates contigs that exhibited ≥2-fold change under dark when 4 μM H2O2 was added to the culture.
Up/down-regulation in Chl. indicates contigs that exhibited ≥2-fold change upon illumination when feeding on E. coli with chlorophyll a but exhibited a compromised change (the light/dark ration became less than the half of amoebae feeding on E. coli with chlorophyll) when feeding on E. coli without chlorophyll. (C) Categorization of GO terms into 10 categories based on their functions. Categories highlighted in orange are enriched in upregulated contigs while categories highlighted in light blue are enriched in downregulated contigs when amoebae feeding on green prey were illuminated. Colored
corresponds to one contig. For example, there are five contigs encoding glutathione peroxidase in Naegleria sp. (N) while only one contig in Acanthamoeba sp. (A) and Vannella sp. (V). Numbers in the graph indicates total of the FPKM values in respective conditions.
A B
LightDark
D
Light
*
p ≦ 0.05Dark0 10 20 30
0 1 2 3 4
Light (-2.73 h-1)
0 4 8 12 16
0 1 2 3 4
Relative FM1-43 intensity in amoebae (per area)
Times of co-culture (h)
Times of co-culture (h)
C
LightDark
Dark (-1.42 h-1)
Light (-5.28 h-1)
Dark (-4.49 h-1)
Relative FM1-43 intensity in amoebae (per area)
0 h 4 h
0 h 4 h
0 20 40 60 80 100
0 1 2 3 4
Percentage of amoeba cells
*
*
Negleria sp.+Green Negleria sp.+Pale
Number of beads engulfed by an amoeba cell 0 1 2 3 4
0 bead 1 bead
2 beads 3 beads
Negleria sp.+Green (FM1-43)
Negleria sp.+Pale (FM1-43) Negleria sp.+Green (FM1-43)
Negleria sp.+Pale (FM1-43) Negleria sp.+Beads
Figure 3.2. Effects of the photosynthetic trait of bacterial prey on engulfment and digestion of prey by Naegleria sp.
(A, B) Naegleria sp. was co-cultured with green or pale S. elongatus prey under dark and
beads (green fluorescence). (B) Comparison of number of fluorescent beads engulfed by amoeba cells in respective co-cultures. The error bar represents the standard deviation of three biological replicates. (C, D) Naegleria sp. was co-cultured with green or pale S. elongatus prey that was stained with the green fluorescent dye FM1-43 under dark, and then cells and preys were stuck on MAS-coated cover glass to inhibit amoebae to newly engulf bacterial prey. Then (hour 0) the cells were kept under dark or transferred to light (200 μE m-2 s-1) for 4 h. (C) Micrographs showing amoeba cells (phase-contrast)
digesting green or pale S. elongatus prey (FM1-43 green fluorescence) under dark or light condition. Images at hour 0 and 4 are shown. (D) Quantification of decrease in FM1-43 fluorescence from prey that had been engulfed by amoebae by hour 0 (rate of digestion) in respective conditions. The error bar represents the standard deviation of three biological replicates. Scale bars = 20 μm (A, C).
Oxidative stress response 1
Catalase
1,000
0 500
600
0 300
300
0 150
1,000 500
600 300
300 150
0 500
1,000 500
0 500
1,000 500
600
0 300
600 300
600
0 300
600 300
0 150
300 150
1
2
1 12
N A
V
1761751801633
1,132
543
955
500 884
569 1,117
1,764
753
726 660
551
N1 comp192408_c0_seq1|m.4650 N2 comp174950_c0_seq1|m.10133 A1 comp188885_c0_seq1|m.25786 A2 comp188885_c0_seq1|m.25787 V1 comp123359_c0_seq1|m.13841
1,000
0 500
600
0 300
300
0 150
500 600
300 150
219153
168
64 665
616 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Thioredoxin
20,000
0 10,000
800
0 400
2,000
0 1,000
400
0 200
600
0 300
20,000 10,000
800 400
2,000 1,000
400 200
600 300
0 10,000
10,000
0 10,000
10,000 0 400
800 400
0 400
400
2,000
0 1,000
2,000 1,000
2,000
0 1,000
1,000
0 300
600 300 20,000
6 5 4 3 2 V1
1,121
1,008
1,270
1,405 3,314
2,456
4,211
3,152 2,329 6,785
3,767
4,138
3,872 3,082
N1 comp222740_c10_seq1|m.26011 N2 comp215338_c0_seq1|m.23334 N3 comp218001_c0_seq1|m.3573 N4 comp217802_c0_seq1|m.12789 N5 comp214336_c0_seq1|m.23096 N6 comp223805_c0_seq1|m.9397 N7 comp212182_c0_seq1|m.21773 N8 comp229501_c0_seq1|m.21674 A1 comp191596_c1_seq2|m.42213 A2 comp191030_c0_seq1|m.46136 A3 comp188618_c0_seq1|m.31761 A4 comp197048_c0_seq1|m.7755 A5 comp192368_c0_seq1|m.33075 A6 comp194676_c0_seq1|m.19143 A7 comp190977_c1_seq1|m.39093 A8 comp191774_c0_seq1|m.37757 A9 comp195144_c0_seq1|m.32433 A10 comp193291_c1_seq4|m.35492 A11 comp193004_c0_seq1|m.19663 V1 comp122719_c0_seq1|m.34782 V2 comp118199_c0_seq1|m.31505 V3 comp121352_c1_seq1|m.29457 V4 comp124849_c0_seq1|m.14768 V5 comp124069_c0_seq1|m.31318 V6 comp129006_c3_seq1|m.23320 20,000
0 10,000
800
0 400
2,000
0 1,000
600
0 300
10,000 400
2,000
1,000 300
981
669 2,935
2,062 8,003
3,102 20,000
20,000
20,000
0 200
400 200
0 200
400 200
0 200
200 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Superoxide dismutase
6,000
0 3,000
300
0 150
3,000
0 1,500
6,000 3,000
300 150
3,000 1,500
0 150
300 150
0 150
300 150
0 1,500
3,000 1,500
3 2 1 4 3 2 1
3 2 1
N A
V
2,762
2,644
2,910
2,669 433
305
394
377 207
167 1,843
1,367
1,321
1,073 948
928
N1 comp160733_c0_seq1|m.20402 N2 comp197010_c0_seq1|m.19572 N3 comp197010_c1_seq1|m.19300 N4 comp218227_c0_seq1|m.7624 A1 comp188230_c0_seq1|m.40801 A2 comp188346_c0_seq1|m.30103 A3 comp132351_c0_seq1|m.39071 V1 comp121193_c0_seq2|m.27450 V2 comp117429_c0_seq1|m.23863 V3 comp122599_c0_seq1|m.22457
Contig
0 150
3,000
0 1,500
300
150 1,500
2,737
3,183 368
320 3,194
1,801 0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
ND
ND
Oxidative stress response 2
Ascorbate peroxidase
600
0 300
600 300
V1
V1 comp122783_c0_seq1|m.3926
517577
0 300
600 300
0 300
600 300
461511463448
Green (rep. 2)PaleFPKM Green (rep. 1)
Peroxiredoxin
16,000
0 8,000
5,000
0 2,500
1,500
0 500
16,000 8,000
5,000 2,500
1,000
500
0 8,000
16,000 8,000
0 8,000
16,000 8,000
0 2,500
5,000 2,500
0 2,500
5,000 2,500
3 2
1 12345678
5 4 3 2 1
N A
V
2,328
1,779
2,416
2,307 3,482
2,581
5,788
7,273 2,670
2,244 10,461
7,871
9,390
8,577 3,980
2,833
N1 comp161327_c0_seq1|m.21473 N2 comp196746_c0_seq1|m.16621 N3 comp225147_c1_seq1|m.3590 A1 comp190305_c0_seq1|m.42848 A2 comp191074_c1_seq1|m.50692 A3 comp197629_c1_seq1|m.44286 A4 comp184213_c1_seq1|m.49637 A5 comp193391_c0_seq4|m.23221 A6 comp189344_c0_seq2|m.39712 A7 comp193418_c0_seq1|m.21148 A8 comp193037_c0_seq1|m.37269 V1 comp118373_c0_seq1|m.26901 V2 comp123133_c0_seq1|m.25027 V3 comp118911_c0_seq1|m.29873 V4 comp126377_c0_seq2|m.11535 V5 comp127697_c0_seq2|m.5968 16,000
0 8,000
5,000
0 2,500
1,000
8,000 2,500
2,840
2,735 2,444
1,695 15,790
7,651
1,500
0 500 1,000
500 1,000 1,500
0 500 1,000
500 1,000 1,500 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Glutaredoxin
6,000
0 3,000
600
0 300
300
0 150
6,000
3,000 300 150
0 3,000
6,000 3,000
0 3,000
6,000 3,000
600
0 300
300 600
0 300
600 300
3 2 1
4 3 2 1
3 2
N1 A
V
303
357
390
384
9626187471,090550340
605
322
606
689 1,269
1,297
N1 comp197043_c0_seq1|m.26229 N2 comp196883_c0_seq1|m.24409 N3 comp221174_c0_seq1|m.16477 A1 comp199540_c0_seq1|m.12891 A2 comp127545_c0_seq1|m.49958 A3 comp189732_c0_seq1|m.39341 V1 comp117553_c0_seq1|m.45875 V2 comp122551_c0_seq1|m.17789 V3 comp120750_c0_seq1|m.35507 V4 comp129187_c1_seq1|m.1393
Contig
6,000
0 3,000
600
0 300
300
3,000 300
581
273
962618
806
567 6,000
6,000
6,000
300
0 150
150 300 300
0 150
150 300 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Glutathione peroxidase
1,000
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500
4 3 2 N1
593
253
859
441 993
587
N1 comp197051_c1_seq2|m.22797 N2 comp227059_c0_seq3|m.1915 N3 comp226183_c1_seq1|m.3708 N4 comp230203_c0_seq1|m.20301 A1 comp190730_c0_seq1|m.38776 V1 comp118319_c0_seq2|m.24239 1,000
0 500
500 1,292
505 1,000
1,000
1,000
800
0 400
1,000
0 500
800
400 500
0 400
800 400
0 400
800 400
1,000
0 500
1,000 500
1 1
A V
678311270547
17255235488147
0 400
1,000
0 500
800
400 500
892123
6412621
Contig
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
NDND
Oxidative stress response 3
Glutathione synthetase
400
0 200
150
0 50
100
0 50
400
200 50
100 50
0 200
400 200
0 200
400 200
100
0 50
100 50
1 1
1
N A
V
75807856
936155336745
341236264135
N1 comp170906_c0_seq1|m.12558 A1 comp198022_c1_seq5|m.13728 V1 comp126782_c0_seq1|m.13264
400
0 200
100 150
100
0 50
200
100 50
89102
16168
3731
100
0 50
50 100 150 100
0 50
50 100 150 100
0 50
50 100 150 100 150
150
150 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Glutathion S-transferase
3,000
0 1,500
1,000
0 500
3,000 1,500
0 1,500
3,000 1,500
0 1,500
1,500
1,000 500
0 500
1,000 500 3,000
3,000 123
V
1,674
1,653
1,628
1,405
N1 comp222120_c0_seq1|m.19841 N2 comp215852_c0_seq1|m.19804 N3 comp220161_c1_seq1|m.17653 N4 comp219327_c0_seq1|m.18450 N5 comp171992_c0_seq1|m.19016 N6 comp219524_c0_seq1|m.20621 A1 comp188728_c0_seq1|m.30477 A2 comp190111_c0_seq1|m.44542 A3 comp193211_c0_seq1|m.42968 A4 comp191147_c0_seq2|m.40291 A5 comp190522_c0_seq1|m.39396 A6 comp191234_c0_seq2|m.34399 V1 comp98094_c0_seq1|m.26854 V2 comp106525_c0_seq1|m.37532 V3 comp125662_c0_seq1|m.37473 3,000
0 1,500
1,000
0 500
3,000
1,500 500
1,608
1,244 200
0 100
200 100
4,660
2,137
1,704
2,025 1,238 2,960
1,628 0 100
200 100
0 100
200 100
0 100
100 20,000
0 10,000
500
0 250
20,000 10,000
500 250
0 250
500 250
0 250
250 9,870
6,214
9,645
4,091 2,906 500
0 250
250 8,895
4,682 0
10,000
20,000 10,000
0 10,000
20,000 10,000
0 10,000
10,000 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Carbonyl reductase
5,000
0 2,500
1,500
0
1,000 600
0 500 300
5,000 2,500
1,500 1,000
500 300
5,000
0 2,500
5,000 2,500
0 2,500
5,000 2,500
0 1,000 500
1,500 1,000 500
0 1,000 500
1,500 1,000 500
1
4 3 2 1
5 4 3 2 N A1
V
692
627
634
863 1,160
190
1,729
364 639
92
1,0141041,11911631
N1 comp222757_c0_seq1|m.17440 A1 comp193008_c0_seq1|m.24805 A2 comp195979_c0_seq1|m.27346 A3 comp192631_c0_seq2|m.37586 A4 comp190819_c0_seq1|m.38965 A5 comp193008_c0_seq1|m.24804 V1 comp126764_c0_seq1|m.31102 V2 comp121793_c0_seq1|m.35963 V3 comp122682_c0_seq2|m.16871 V4 comp121793_c1_seq1|m.39085
Contig
0 2,500
1,500
0 1,000
600
500
2,500 1,000
500
1,216
485 1,893
476
1,81756
0 300
300 600
0 300
300 600 600 600 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
ND 16
Oxidative stress response 4
Apolipoprotein D
1,500
0 1,000
6,000
0 3,000
6,000
0 3,000
500
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
6,000 3,000
6,000
0 3,000
6,000 3,000
1 1
2 1
N A
V
7,2712181916,550
1,1373455,5496832,18340
264522924251
N1 comp222513_c0_seq1|m.20128 A1 comp190312_c0_seq1|m.15969 V1 comp121626_c1_seq1|m.13488 V2 comp122886_c0_seq3|m.29006 500
6,000
0 3,000
6,000
0 3,000
3,000 6,000 3,000
49
1,378479
7444
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) 7,817
Cob(I)yrinic acid a,c-diamide adenosyltransferase
100
0 50
200
0 100 100
50
100
1 123
2 1
N A
V
22512417624
211
57
258
85 243
93
7215681062453
N1 comp196062_c0_seq1|m.19674 A1 comp197065_c0_seq1|m.46818 A2 comp191458_c0_seq1|m.41844 A3 comp197065_c3_seq1|m.56742 V1 comp121578_c0_seq1|m.24164 V2 comp122692_c2_seq1|m.6280 150
150
478160
83
10431
100
0 50
100 50
150 150
100
0 50
100 50
150 150
100
0 50
100 50
150 150
200
400
0 200
200 400 200
0 100
100 200
200
0 100
100 200 200
0 100
100 200
400
0 200
200 400 400
0 200
200 400 474 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
NADP-reducing hydrogenase subunit HndC
50
0 25
50 25
A1
2415
A1 comp192699_c1_seq1|m.38895
4531
0 25
50 25
0 25
50 25
0 25
50 25 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
Contig
NDND
Peptide methionine sulfoxide reductase
4,000
0 2,000
4,000
0 2,000
2,000
0 1,000
4,000 2,000
4,000
0 2,000
4,000 2,000
0 2,000
4,000 2,000
4,000 2,000
4,000
0 2,000
4,000 2,000
4,000
0 2,000
4,000 2,000
2,000 1,000
2,000
0 1,000
2,000 1,000
2
1 12
2 1
N A
V
1,5718258931,935
2,4232454,7867692,365173
2,9494685631,783284
N1 comp161358_c0_seq1|m.4904 N2 comp224705_c0_seq2|m.7781 A1 comp191467_c0_seq1|m.39140 A2 comp196146_c1_seq1|m.42352 V1 comp107284_c0_seq1|m.23595 V2 comp121801_c1_seq1|m.29460
0 2,000
4,000
0 2,000
2,000
0 1,000
2,000 4,000 2,000
2,000 1,000
492
1,591108
4,2925164,232 2,955
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Phytoene desaturase
2,000
0 1,000
3,000
0 1,500
1,000
3,000 1,500
1,000 0 1,000 2,000
0 1,000
2,000 1,000
0 1,500
3,000 1,500
0 1,500
3,000 1,500
1 N1 A
2,847612,7902201,8588
5102658981,2783
N1 comp217346_c0_seq1|m.11870 A1 comp194869_c0_seq1|m.28844
2,000
0 1,000
3,000
0 1,500
2,000 1,000 1,500
72612
7989
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Geranylgeranyl pyrophosphate synthase
300
0 150
200
0 100
80
0 40
300 150
200 100
80 40
0 150
300 150
0 150
150 0 100
200 100
200
0 100
200 100 0 100
200 100
200
0 100
100 0 100
100 0 40
80 40
2 V1
111
113
88
53
1453221110283
1919131936
N1 comp213578_c0_seq1|m.14664 A1 comp194723_c0_seq1|m.21777 V1 comp124726_c1_seq1|m.28171 V2 comp124726_c0_seq1|m.31417
300
0 150
200
0 100
80
0 40
150 200 100 40
0 100
200 100
114
119
12121
255155
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Bifunctional lycopene cyclase/phytoene synthase
600
0 300
600 300
600
0 300
600 300
600
0 300
300
6882226831315
600
0 300
600 300
33213
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Zeaxanthin epoxidase
600
0 300
600 300
0 300
600 300
V1
268114130223
V1 comp124759_c0_seq1|m.21868 600
0 300
300
560110
Green (rep. 2)PaleFPKM Green (rep. 1)
Carotenoid synthesis
Carotene epsilon-monooxygenase
200
0 100
100
0 50
60
0 30
200 100
100 50
60 30
0 100
200 100
0 100
200 100
0 50
100 50
0 50
100 50
60
0 30
60 30
1
2 1 2 N1 A
V
332520
169
115
125
68 119
99 99
113
86 188
168
23 N1 comp221700_c0_seq1|m.16996 N2 comp225590_c0_seq1|m.8817 A1 comp195139_c0_seq1|m.35379 A2 comp193039_c0_seq1|m.25641 V1 comp123304_c0_seq1|m.11152
Contig
200
0 100
100
0 50
60
0 30
100 50
60 30 91
50 151
204
33100
100
100
56
58
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Contig
DNA repair 1
ALKB
80
0 40
500
0 250
30
0 15
80 40
500 250
500
0 250
500 250
500
0 250
500 250
30 15
30
0 15
30 15
1
1 12345
N A
V
328
506 638 272 227 316 357
33 30 10 9 10
11 N1 comp220611_c0_seq1|m.15695
A1 comp193431_c0_seq2|m.37977 A2 comp201113_c0_seq1|m.23453 A3 comp192571_c0_seq2|m.34799 A4 comp191748_c0_seq1|m.40438 A5 comp193585_c0_seq1|m.38092 V1 comp128387_c2_seq1|m.30113
Contig
500
0 250
30
0 15
500 250
30 15
1916
447 409
16 80 21
0 40
80 40
80
0 40
80 40
80
0 40
80 40 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
DNA-(apurinic or apyrimidinic site) lyase
100
0 50
500
0 250
100 50
500 250
0 250
500 250
1
A1 V
283335
3510.253 N1 comp225006_c0_seq1|m.7768 A1 comp199388_c0_seq1|m.9331 V1 comp126066_c0_seq2|m.29588 150
150 500
0 250
250
28456
0
100
0 50
100 50 150
150 100
0 50
100 50 150
150 100
0 50
100 50 150
150
57
FPKM 151
Deoxyribodipyrimidine photo-lyase
1,000
0 500
400
0 200
500 400 200
400
0 200
400 200
1 2 1
N V
132
9
4
152
0.42900.0682105 N1 comp222533_c0_seq1|m.15479 V1 comp125035_c0_seq1|m.12561 V2 comp127813_c1_seq1|m.15993
1,000 400
0 200
400 200
713
4
0.8388
1,000
0 500
500 1,000 1,000
0 500
500 1,000 1,000
0 500
500 1,000
Green (rep. 2)w/o preyPaleGreen (rep. 1)FPKM
GT -mismatch-specific thymine DNA glycosylase
100
0 50
100 50
100
0 50
100 50
100
0 50
100 50
A1
6919891101549
A1 comp196193_c1_seq1|m.16160
100
0 50
100 50
3620
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
ND ND ND
Contig
0
N1 7 513 28 5 29
10 81
Green (rep. 2)w/o preyPaleGreen (rep. 1)
200 100
200 100
200
0 100
200 100
200
0 100
200 100
200
0 100
200 100
MCM8
40
0 20
40 20
A1
321412113024
A1 comp197416_c1_seq3|m.39014
4032
40
0 20
40 20
40
0 20
40 20
40
0 20
40 20 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Msh2
100
0 50
100 50
N1
182410112216
N1 comp225420_c0_seq1|m.4740
1925
0 50
100 50
0 50
100 50
0 50
100 50 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
RHP23
200
0 100
200 100
2 A1
303
143
161
107 173
110
A1 comp191210_c0_seq1|m.31519 A2 comp193102_c0_seq1|m.31176
371
242 200
0 100
200 100
200
0 100
200 100
200
0 100
200 100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
RHP26
60
0 30
20
0 10
30 20 10
20
0 10
20 10
V1
4162223
48
33
58
22 33
A1 comp198392_c1_seq1|m.38884 A2 comp198240_c0_seq1|m.8513 A3 comp198384_c0_seq1|m.21338 V1 comp127772_c1_seq3|m.15332
60 20
0 10
20 10
129
96
64 60
0 30
30 60 60
0 30
30 60 60
0 30
30 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
RAD5
80
0 40
80 40
200
0 100
200 100
0 100
200 100
0 100
100 71
77
64
53 111
2222191123
N1 comp218612_c0_seq1|m.4221 A1 comp198679_c3_seq1|m.9138 A2 comp198190_c0_seq1|m.23434 A3 comp198158_c0_seq2|m.16420 A4 comp199095_c1_seq2|m.895
200
0 100
100 139
121
3324
0 40
80 40
0 40
80 40
0 40
40 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig Contig
ND NDND ND ND
DNA repair 2
RAD23
200
0 100
60
0 30
200
100 30
1
2 A1
V
4645
303
143
161
107 173
110
A1 comp191210_c0_seq1|m.31519 A2 comp193102_c0_seq1|m.31176 V1 comp123008_c0_seq1|m.15170
60 371
242 200
0 100
200 100
200
0 100
200 100
200
0 100
200 100
60
0 30
30 60 60
0 30
30 60
45595543
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
RAD51
500
0 250
600
0 300
150
0 100 50
500 250
600 300
150 100 50
0 100 50
150 100 50
2 1
1 1234
N A
V
173
284
191
199 468
394
304
346 156
190 24
25
24
44 28
29
N1 comp196015_c0_seq1|m.15894 A1 comp191531_c0_seq1|m.35713 A2 comp193435_c0_seq1|m.35060 A3 comp193485_c0_seq1|m.30492 A4 comp193490_c0_seq1|m.17298 V1 comp123680_c0_seq1|m.30158 V2 comp123680_c1_seq1|m.29099
Contig
150
0 100 50
100 50
114
134 676
649 29
38 500
0 250
500 250
500
0 250
500 250
500
0 250
500 250
0 300
600 300
0 300
600 300
0 300
600 300 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
DNA repair 3
Contig
ND
RAD16
30
0 15
30 15
30
0 15
30 15
30
0 15
30 15
2 A1
27
30
12
11 36
18
A1 comp198719_c2_seq3|m.20527 A2 comp198158_c0_seq2|m.16420
30
0 15
30 15
66
36 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
ND ND
XRCC
200
0 100
200 100
N1 51 57 27 16 11
24 N1 comp221477_c2_seq1|m.17537
18 13
0 100
200 100
0 100
200 100
0 100
200 100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Respiration 1
ATP/ADP translocase
Contig
2,000
0 1,000
100
0 50
150,000
50,000 100,000
0 150
0 100 3,000
0 50 1,500
2,000 1,000
100 50
0 50
100 50
0 50
100 50
150,000 50,000 100,000
50,000 100,000
0
150,000 50,000 100,000
50,000 100,000
0
150,000 50,000 100,000
150 100 50
0 100 50
150 100 50
0 100 50
150 100 50
3,000 1,500
3,000
0 1,500
3,000 1,500
1 12
2 1
2 3
N A
V
4,651 5,156 4,770 5,699
8,9679,42823,23325,49314,99610,906
1,1471,1221,076798807 N1 comp196908_c0_seq1|m.19210
N2 comp222692_c0_seq1|m.11667 A1 comp184183_c1_seq1|m.43123 A2 comp184183_c0_seq1|m.50894 A3 comp192344_c0_seq1|m.28367 V1 comp118217_c0_seq1|m.19347 V2 comp118217_c0_seq1|m.19348 100
0 50
150,000
50,000 100,000
0 150
0 100 3,000
0 50 1,500
50 50,000 100,000 100
50 3,000 1,500
3,347 3,523
3,3433,510
718635
0 1,000
2,000 1,000
0 1,000
2,000 1,000
0 1,000
2,000 1,000
1,054
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
COX11
300
0 150
200
0 100
300 150
0 150
300 150
0 150
300 150
200 100
0 100
200 100
1 1
A V
46391446
581918728141171 A1 comp193195_c0_seq1|m.37792 V1 comp122488_c0_seq2|m.24697
300
0 150
200
0 100
150 100
19
24160 181
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
COX15
400
0 200
100
0 50
400 200
400
0 200
400 200
400
0 200
200 100
50
100
0 50
100 50
V1
239616
681773
981719419125 N1 comp228272_c0_seq1|m.12304 A1 comp192893_c0_seq1|m.25498 V1 comp125185_c0_seq2|m.16544
400
0 200
100
0 50
400 200
100 50
5106
11131 2542319153
500
0 250
500 250
0 250
500 250
0 250
250 500
0 250
250 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
COX19
60
0 30
60 30
4016811162219
0 30
60 30
0 30
60 30
0 30
30 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
SCO1
200
0 100
100
0 50
200 100
200
0 100
200 100
200
0 100
100 100
50
V1
975878
75142163102226 A1 comp197690_c0_seq3|m.5845 V1 comp107275_c0_seq1|m.22652
200
0 100
150
200 100
47141
32226
150
100
0 50
100 50
150 100
0 50
100 50
150
119
114
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Respiration 2
Prohibitin 2
200
0 100
1,000
0 500
500
0 250
200 100
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
250
500
0 250
500 250
1 1
1
N A
V
53945999 334137152233
86115
N1 comp227900_c0_seq1|m.15768 A1 comp192167_c0_seq1|m.37994 V1 comp122381_c0_seq1|m.21229
1,000
0 500
500
0 250
1,000
500 250
70257 123468
0 100
200 100
0 100
200 100
0 100
200 100
4655451,2331,1854841,024435935
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Prohibitin 3
0 400 200
400 200
V1
330275289263
V1 comp122032_c1_seq1|m.33351
168396
0 400 200
400 200
0 400 200
400 200 Green (rep. 2)PaleFPKM Green (rep. 1)
TIM10
50
0 25
50 25
50
0 25
50 25
50
0 25
50 25
A1
3066767418
A1 comp190184_c0_seq3|m.41328
Contig
50
0 25
50 25
060
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM14
0 500
0 250 100
50
100 50
500 250
0 250
500 250
0 250
500 250
1 1
N A
59457910914285
507123201741 N1 comp220797_c0_seq1|m.5849 A1 comp192514_c0_seq1|m.44559
500
0 250
250
11461
3390
0 100 50
100 50
0 100 50
100 50
0 100 50
100 50 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM16
400
0 200
400 200
2 A1
88 142185 168 68
250 A1 comp181094_c0_seq2|m.48439 A2 comp184602_c0_seq1|m.48738
128 400479
0 200
400 200
400
0 200
400 200
400
0 200
400 200 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Contig Contig Contig
Prohibitin 1
300
0 150
1,000
0 500
1,000
0 500
300 150
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
1,000 500
1 1
1
N A
V
527444464497
2883516686534561,214
7810927422961 N1 comp228209_c0_seq1|m.19680 A1 comp189959_c0_seq1|m.42468 V1 comp122032_c0_seq1|m.30636
1,000
0 500
1,000 500
391852
277711
72197
300
0 150
300 150
300
0 150
300 150
300
0 150
300 150
0 500
1,000 500
0 500
1,000 500 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
115
Respiration 3
TIM23
200
0 100
100
381804377155
200
0
200
0 100
100 200 200
0 100
100 200 200
0 100
100
197
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM44
80
0 40
150
0 100 50
50 40
0 40
80 40
0 40
150 100 50
150
0 100 50
150 100 50
150
0 100 50
50
1671081023893
4518131424 80
0 40
150
0 100 50
80 40
150 100 50
48135
2757
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM50
200
0 100
100
0 50
200 100
100 50
100
0 50
100 50
100
0 50
50 14674
68 110 108
73757337103 N1 comp168559_c0_seq1|m.14233 N2 comp221198_c0_seq1|m.14508 A1 comp191345_c0_seq1|m.34823
100
0 50
100 50 103 194
67105
200
0 100
200 100
200
0 100
200 100
200
0 100
100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TOM40
100 0 50
200
0 100
100 50
200 100
200
0 100
200 100
200
0 100
100
16622221475161
114101746078
150
150 200
0 100
200 100
2389
67109
100 0 50
100 50 150
150 100
0 50
100 50 150
150 100
0 50
50 150 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM17
30
0 15
600
0 300
30 15
600 300
100
0 50
100 50
100
0 50
100 50
1 1
1
N A
V
124129
73127254231122496
515714621 N1 comp186302_c0_seq1|m.19129 A1 comp178054_c1_seq1|m.47330 V1 comp120032_c0_seq1|m.21088
100
0 50
100 50
100
113657
422
30
0 15
30 15
30
0 15
30 15
30
0 15
30 15
600
0 300
600 300
600
0 300
600 300
600
0 300
600 300
104106136
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM21
200
0 100
200 100
A1
A1 comp190408_c0_seq1|m.49523 200
0 100
200 100
200
0 100
200 100
200
0 100
200 100
2312151731380197
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
TIM22
80
0 40
80 40
80
0 40
80 40 100
0 50
50
1 V1
A
86563333
532368891830 A1 comp195111_c0_seq1|m.20430 V1 comp122494_c0_seq1|m.24138
80
0 40
80 40 100
2925
8396
100
0 50
50 100 100
0 50
50 100 100
0 50
50 100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig Contig
89
Vacuolar-type H+-ATPase 1
V-ATPase subunit A
1,000
0 500 1,000
0 500
1,000 500
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
600
0 300
600 300
0 300
600 300
2 1
1
3 2 N A1
V
474414444549
1,390 1,323 1,271 1,310 872 1,601
288 902 986 597
316
709 N1 comp227542_c0_seq1|m.10798
N2 comp221051_c0_seq1|m.7823 A1 comp191255_c1_seq1|m.27470 A2 comp191255_c0_seq1|m.47522 A3 comp198416_c0_seq4|m.11027 V1 comp122318_c0_seq1|m.10042
1,000
0 500
1,000 500
600
0 300
300
306416
183 249
351 1,000 609
0 500
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
V-ATPase subunit B
0 1,500
0 500
0 250 1,000
500 3,000
1,000 500
0 1,000 500
1,000 500
0 1,000 500
1,000 500
250
1 1
1
N A
302248 V383384318378
1,4227831,2221,188976984
5526491,054872
N1 comp196952_c0_seq1|m.13622 A1 comp192402_c0_seq1|m.25067 V1 comp120287_c0_seq1|m.10889
0
500 1,000
500
1,000 500
382
2,4271,699
442692
1,500 3,000 1,500 0 1,500 3,000 1,500 0 1,500 3,000 1,500 0 1,500 3,000
500
0 250
250 500 500
0 250
250 500
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) 472
V-ATPase subunit C
2,000
0 1,000
2,000
0 1,000
300
0 150
2,000 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000 2,000
0 1,000
2,000 1,000
300 150
300
0 150
300 150
2 1
1
2 N1 A
V
273309255271
1,533 1,333 2,768 2,482 970 1,919
194 203 252 362 170
202 N1 comp196930_c0_seq1|m.11356 N2 comp196942_c0_seq1|m.21462 A1 comp176844_c0_seq1|m.42008 A2 comp191778_c0_seq2|m.28473 V1 comp121935_c0_seq1|m.15701
2,000
0 1,000
300
0 150
2,000 1,000
300 150
243286
302 612
344 2,000 805
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
V-ATPase subunit D
0
600
0 300 600
300
600 300
600 300
600
0 300
600 300
N 1,000
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500
1 123
2 1
A
V
1,221
974 859 1,080
767 1,004 2,146 2,032 783 1,593
266262335329181271 N1 comp196607_c0_seq1|m.18535 A1 comp190948_c0_seq1|m.30663 A2 comp188929_c0_seq1|m.37071 A3 comp188929_c0_seq1|m.37072 V1 comp122459_c0_seq1|m.14005 V2 comp123814_c0_seq1|m.8010 600
0 300
600 300 1,000
0 500
500
684 922
904 1,220
233340
0 300
600 300
0 300
600 300
0 300
600 300 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
Contig Contig
Vacuolar-type H+-ATPase 2
V-ATPase subunit a
300 150 0
100
0 50
150
300 150 0
300 150
150 0 150
100 50
0 50
100 50
V1
77615963
162260309151310
300 150 0
100
0 50
150 50
37
3556 95
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
V-ATPase subunit E
500
0 250
2,000
0 1,000
2,000
0 1,000
500 250
0 250
500 250
0 250
500 250
2,000 1,000 1,000
0 1,000
2,000 1,000
1 1
1
N A
V
1,5091,4411,4221,741
644787791
300308453305222346 N1 comp227605_c0_seq1|m.19734 A1 comp184086_c0_seq1|m.40729 V1 comp118997_c0_seq1|m.17107
500
0 250
2,000 2,000
0 1,000
250 1,000
9911,150
402892
269343 2,000 0 1,000
1,000 2,000 2,000
0 1,000
1,000 2,000 2,000
0 1,000
1,000 2,000
169920571578
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
V-ATPase subunit F
600
0 300
1,000
0 500
1,000
0 500
600 300
600
0 300
600 300
600
0 300
600 300
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
1,000 500
1,000
0 500
1,000 500
1 1
N1 A
394642309217327 V493868368421
4533941,089750462815
453
N1 comp227723_c0_seq1|m.25000 A1 comp188094_c0_seq1|m.44297 V1 comp125494_c0_seq1|m.33170
600
0 300
1,000
0 500
1,000
0 500
600 300
1,000 500
1,000 500
188296 493492
468756
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
V-ATPase subunit G
2,000
0 1,000
2,000 1,000
0 1,000
2,000 1,000
V1
1,67420451,2021,201
V1 comp120889_c0_seq1|m.32212 2,000
0 1,000
1,000
2,045777925
Green (rep. 2)PaleFPKM Green (rep. 1)
V-ATPase subunit H
150
0 100
2,000
0 1,000
600
0 50 300
100 50 1,000
600 300
2 V1
105104
633 537 491 692
385573583315525 N1 comp158917_c0_seq1|m.13351 A1 comp192911_c0_seq1|m.9326 V1 comp120946_c0_seq1|m.43677 V2 comp120946_c1_seq1|m.18228
150 2,000
149156
775 972
1,4221,971
150
0 100 50
100 50 150 150
0 100 50
100 50 150 150
0 100 50
50 2,000
0 1,000
1000 2,000 2,000
0 1,000
1,000 2,000 2,000
0 1,000
1,000 600
0 300
600 300
600
0 300
600 300
151126133
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
Contig
Vacuolar-type H+-ATPase 3
V-ATPase subunit c’’
217800
0 400
600
0 300
600
0 300
400 600 300
600
0 300
600 300
600
0 300
600 300
600 300
0 300
600 300
1 1
1
N A
V
530289372730557217
126109291368149 555408286394 N1 comp227747_c0_seq1|m.19247 A1 comp177202_c0_seq1|m.42564 V1 comp120031_c0_seq1|m.23662
223
800 600
0 300
600
0 300
600 300 300
9633
106 119306
800
0 400
400 800800
0 400
400 800800
0 400
400 800 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
Proteolysis 1
Cathepsin A
2,000
0 1,000
100
0 50
2,000 1,000
1,000 0
2,000 1,000
1,000 0
2,000 1,000
100 50
1 4 3 2
N1 A
8464626665
301 330 1,058 1,772 687
1,202 N1 comp216944_c0_seq1|m.12834
N2 comp217123_c0_seq1|m.13270 N3 comp217838_c0_seq1|m.13398 N4 comp221953_c0_seq1|m.12720 A1 comp200595_c0_seq1|m.26019
1,000 0
2,000 1,000
112101
434 990 100
0 50
100 50
100
0 50
100 50
100
0 50
100 50
98
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Cathepsin C
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
2 N1 1,177
1,162
2,029
1,513 508
432
N1 comp214966_c0_seq1|m.12794 N2 comp221851_c2_seq3|m.12596
1,500
0 1,000 500
1,500 1,000 500
1,332
712 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Cathepsin B
20,000
0 10,000
0
2,000 100
0 50
500
0 1,000 250
20,000 10,000
20,000
0 10,000
20,000 10,000
20,000
0 10,000
10,000 2,000
1,000 50
500 250
500
0 250
500 250
500
0 250
250 210
237
567
684 378
37,90934,78953,44437,55311,739
N1 comp222264_c1_seq2|m.24062 N2 comp222264_c0_seq2|m.18254 N3 comp161120_c0_seq1|m.21113 N4 comp196690_c1_seq1|m.20318 N5 comp196690_c0_seq1|m.25763 N6 comp161120_c1_seq1|m.24792 N7 comp222291_c0_seq1|m.19331 N8 comp219614_c1_seq1|m.18120 N9 comp224223_c0_seq1|m.11597 A1 comp192370_c0_seq1|m.36718 A2 comp197700_c0_seq1|m.9917 A3 comp195746_c1_seq1|m.28322 A4 comp196648_c0_seq6|m.14151 20,000
0 10,000
100 500
0 250
20,000
10,000 250
212
296
21,95114,048
0 2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
0 2,000 1,000
1,000
100
0 50
50 100 100
0 50
50 100 100
0 50
50 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Cathepsin F
300
0 150
300 150
N1
18316210681
N1 comp221740_c0_seq1|m.7856
142134
0 150
300 150
0 150
300 150
0 150
300 150
229255
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig Contig
NC
Cathepsin Z
800
0 400
1,500
0 1,000 500
800 400
0 400
400 800
0 400
800 400
1,500 1,000 500
0 1,000 500
1,500 1,000 500
2 1
4 3 2 N1
V
2,138
1,777
2,310
2,627 1,100
1,133
1,803
1,709 756
867
N1 comp171747_c0_seq1|m.20352 N2 comp212828_c0_seq1|m.20688 N3 comp214909_c0_seq1|m.27463 N4 comp214909_c1_seq2|m.21648 V1 comp124789_c4_seq1|m.30912 V2 comp124789_c0_seq1|m.36485
800
0 400
1,500
0 1,000 500
400 1,000
500 2,050
1,681 976
1,035 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Chymotrypsin
500
0 250
250
3 2 N1
N1 comp227093_c0_seq1|m.4050 N2 comp224595_c1_seq1|m.18363 N3 comp224121_c0_seq1|m.5208
500
0 250
250 500
0 250
250 500
0 250
250 500 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Proteolysis 2
NDND NDND 188
279
55
15 309
223 169
81
Contig Contig
Cathepsin L
6,000
0 3,000
10,000
0 5,000
500
0 250
3,000
0 1,500
400
0 200
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
10,000 5,000
500 250
0 250
500 250
0 250
500 250 0
5,000
10,000 5,000
0 5,000
10,000 5,000
400 200 3,000 1,500
3,000
0 1,500
3,000 1,500
0 200
400 200 6,000
6,000 1
3 2
1 1234 5678910
4 3 2
N A
V
3,813
3,667
3,293
3,269 13,923
12,617
10,580
11,798 7,449
7,440 3,413
6,525
4,023 1,694
1,671 3,740
6,000
0 3,000
10,000
0 5,000
500
0 250
3,000
0 1,500
400
0 200
3,000 5,000 250 200
3,000 1,500
1,970
2,485 9,691
9,722 2,176
3,038 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
N1 comp227258_c0_seq1|m.16318 N2 comp196035_c1_seq1|m.18909 N3 comp217656_c0_seq1|m.16225 A1 comp184181_c0_seq1|m.37815 A2 comp191394_c1_seq1|m.40371 A3 comp194227_c1_seq2|m.37440 A4 comp192259_c1_seq1|m.47635 A5 comp192261_c1_seq1|m.50689 A6 comp192259_c0_seq1|m.39127 A7 comp193323_c1_seq1|m.26742 A8 comp192261_c2_seq1|m.48742 A9 comp196286_c2_seq2|m.23901 A10 comp198110_c0_seq1|m.2200 V1 comp122919_c1_seq1|m.20448 V2 comp122872_c0_seq1|m.10793 V3 comp124629_c0_seq1|m.18255 V4 comp121275_c0_seq2|m.23570
Contig
ND ND
ND
Squalene monooxygenase
1,000
0 500
100
0 50
1,000 500
100 50
100
0 50
100 50
100
0 50
100 50 0 500
1,000 500
0 500
1,000 500
1 1
2 N1 A
V
287725
1,004
82
16550438 27511092259
10315109
N1 comp216080_c1_seq1|m.5734 N2 comp216080_c0_seq1|m.19550 A1 comp195623_c0_seq1|m.11809 V1 comp122050_c0_seq1|m.9848
1,684
1,000
0 500
100
0 50
500 100
50
75 110
545
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500 1,000
1,236 823
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
L-gulonolactone oxidase
80
0 40
200
0 100
200
0 100
80 40
200 100
200 100
200
0 100
200 100
200
0 100
100 0 40
80 40
0 40
40
V1
25161468
179292458381
374481041
N1 comp220489_c0_seq1|m.13475 A1 comp194339_c0_seq2|m.27513 V1 comp128213_c0_seq2|m.16856
80
0 40
200
0 100
40 200 100
26531
253
478
200
0 100
200 100 200
0 100
200 100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Oxygen reducing metabolisms
Methylsterol monooxygenase
200
0 100
400
0 200
200 100
400 200
0 200
400 200
0 200 200
400 400
400 1
2 1 4 3 2
N1 A
V
294
145
174207280
499
148
323
165
N1 comp228408_c0_seq1|m.17822 N2 comp224022_c0_seq1|m.7534 N3 comp228514_c0_seq1|m.11837 N4 comp218051_c0_seq1|m.11145 A1 comp193498_c0_seq1|m.19446 A2 comp198885_c0_seq1|m.33502 V1 comp121846_c0_seq1|m.24109 400
0 200
400 200
374169
214
30 0
100
200 100
0 100
200 100
0 100
200 100
0 200
400 200
0 200
400 200
0 200
400 200 400
325
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
132
90
156
160 192
152 272
199
Myosin 1
Type VII
80
0 40
200
0 100
80 40
200 100
80
0 40
80 40
80
0 40
80 40
200
0 100
200 100
1
2 A1
V
508712449
26
52 22
13 86
161
A1 comp198938_c1_seq1|m.14393 A2 comp198938_c2_seq2|m.44474 V1 comp128558_c4_seq1|m.2996
80
0 40
200
0 100
80 40
200 100 1336 45
239
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Type I
300
0 150
200
0 100
300
0 150
300 150
200 100
300 150
300
0 150
300 150
300
0 150
300 150
200
0 100
200 100
200
0 100
200 100
0 150
300 150
3 2 1
7 6 5
4 8910
3 2 1
7 6 5
4 89101112 3
2
N A1
V
363
986
708
614 617
1,165
512
687
709
584
N1 comp221724_c0_seq1|m.7380 N2 comp228109_c0_seq1|m.3268 N3 comp222815_c1_seq1|m.8438 A1 comp195149_c2_seq1|m.48654 A2 comp198265_c0_seq3|m.5910 A3 comp194928_c1_seq2|m.24990 A4 comp197586_c5_seq3|m.6533 A5 comp197586_c1_seq1|m.53935 A6 comp197586_c0_seq1|m.46051 A7 comp195149_c0_seq1|m.30309 A8 comp197586_c4_seq1|m.45078 A9 comp197586_c2_seq1|m.43536 A10 comp188183_c0_seq1|m.44484 A11 comp195149_c1_seq2|m.47403 A12 comp194928_c0_seq1|m.39468 V1 comp126827_c3_seq1|m.4894 V2 comp127146_c0_seq1|m.4290 V3 comp127492_c0_seq1|m.28255 V4 comp128338_c0_seq6|m.2630 V5 comp126827_c1_seq1|m.30554 V6 comp127492_c3_seq1|m.2595 V7 comp127492_c2_seq1|m.29676 V8 comp127492_c1_seq1|m.26684 V9 comp126007_c1_seq1|m.21762 V10 comp120344_c0_seq1|m.31275 300
0 150
200
0 100
300
0 150
300 150
200
100 150
375
1,012
585
957 300
300 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Type II
200
0 100
300
0 150
100
0 50
200 100
300 150
100 50
0 100
200 100
0 100
200 100
0 150
300 150
0 150
300 150
100
0 50
100 50
1 1
2 N1 A
V
7712611783
54256131115134228
N1 comp226013_c0_seq2|m.5781 N2 comp152034_c0_seq1|m.18471 A1 comp191373_c0_seq2|m.2351 V1 comp128849_c1_seq2|m.25002
200
0 100
300
0 150
100
0 50
200 100
300 150
100 50
47104
38203
Contig
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig Contig
91
349
275
442 390
366 132
404
ND
27
66 149
188 227
204 14 154
ND
Myosin 2
Other types
300
0 150
200
0 100
150
200 100
0 100
200 100
1
5 4 3 2 1
N V
293 222 238
164 N1 comp224888_c0_seq1|m.3961 V1 comp128849_c2_seq1|m.627 V2 comp126007_c2_seq1|m.27590 V3 comp128558_c3_seq1|m.25085 V4 comp126007_c0_seq1|m.22111 V5 comp126007_c4_seq1|m.28061
300 200
0 100
100 572 313
0 150
150 300
0 150
150 300
0 150
150 300 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
Contig
1261446341471130157
50,000
0 25,000
200
0 100
50,000 25,000
0 25,000
50,000 25,000
0 25,000
50,000 25,000
200 100
0 100
200 100
0 100
200 100
3 2
1 45678910111213 A
78,766 56,172 134,055 88,3608,552 47,764
0 25,000
200
0 100
50,000 25,000
200 100
4,711
200
200
112,617 150,000
0 100,000
400
0 200
100
0 50,000 50
150,000 100,000 50,000
0 100,000 50,000
150,000 100,000 50,000
400 200
400
0 200
400 200
100 50
0 50
100 50
2
1 3 456789101112
V
194,767 216,763 242,639 233,683
150,000
0 100,000
400
0 200
100
0 50,000 50
100,000 50,000
400
200 50
151,581 98,208
Actin
100,000
0 50,000
200
0 100
100
0 50
100,000 50,000
0 50,000
100,000 50,000
0 50,000
100,000 50,000
100
0 100
200 100
0 100
200 100
100 50
0 50
100 50
0 50
100 50
4 3 2 N1 0 50,000
200
0 100
100
0 50
100,000 50,000
200 100
100 50 200
200
200 100
100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1)
N1 comp226268_c0_seq1|m.15372 N2 comp218105_c0_seq1|m.17135 N3 comp212496_c0_seq1|m.10790 N4 comp225048_c0_seq1|m.5103 A1 comp197233_c0_seq1|m.48321
Contig
71,24918,36120,1609,64730,88126,20135,1345,397ND NDND ND ND
V1 comp127126_c1_seq1|m.30423 V2 comp127126_c3_seq1|m.35979 V3 comp121056_c0_seq1|m.15382 V4 comp126422_c0_seq1|m.18167 V5 comp126520_c0_seq1|m.22802 V6 comp124568_c0_seq2|m.11270 V7 comp126591_c0_seq1|m.22524 V8 comp125992_c0_seq2|m.31100 V9 comp123034_c0_seq2|m.25940 V10 comp128124_c0_seq5|m.17121 V11 comp124299_c0_seq1|m.15318 V12 comp126794_c0_seq2|m.26626 A2 comp197233_c3_seq1|m.51575
A3 comp197233_c1_seq1|m.54766 A4 comp192995_c0_seq1|m.38899 A5 comp193353_c0_seq1|m.5798 A6 comp189645_c0_seq1|m.55912 A7 comp191378_c0_seq3|m.30974
A8 comp197190_c1_seq1|m.24458 A9 comp195956_c0_seq1|m.9932 A10 comp198783_c0_seq1|m.13041 A11 comp197962_c1_seq1|m.12530 A12 comp198043_c0_seq5|m.9355 A13 comp195269_c1_seq1|m.31367
Figure 3.3. Comparison of the effect of the photosynthetic trait of bacterial prey on mRNA levels of selected genes among Naegleria sp., Acanthamoeba sp. and
Vannella sp.
Respective amoebae were co-cultured with green or pale S. elongatus prey under dark and then transferred to light (200 μE m-2 s-1). The cultures with green prey were performed twice independently and the both results (rep. 1 and rep. 2) are shown. To examine the effect of illumination that is independent of prey, respective amoebae were cultured in an organic growth medium without prey under dark and then transferred to light (w/o prey). Graphs show the mRNA levels (FPKM values) of contigs that are related to oxidative stress responses, carotenoid synthesis, DNA repair, respiration, v-type proton ATPase, proteolysis, oxygen reducing metabolisms, myosin, and actin under dark (black bar) and light (magenta bar) conditions. Each bar corresponds to one contig. For example, there are four, three, and three contigs encoding superoxide dismutase in Naegleria sp. (N), Acanthamoeba sp. (A), and Vannella sp. (V),
respectively. Numbers in the graph indicate total of the FPKM values in respective conditions. The FPKM values of respective contigs were compared only when the total of values of two comparative conditions were ≥20. Otherwise, the data were defied as not detected (ND). The contig IDs are shown beside each graph.
Oxidative stress responses 1
Superoxide dismutase
0
4 3 2 N1
1,843
1,367
1,321
1,073 948
928
N1 comp160733_c0_seq1|m.20402 N2 comp197010_c0_seq1|m.19572 N3 comp197010_c1_seq1|m.19300 N4 comp218227_c0_seq1|m.7624
3,194
1,801 6,000
0 3,000
6,000 3,000
4 3 2 N1
1,317
1,619
2,047
1,462 6,860
928 1,771
1,653 0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Catalase
0
2 N1 1,117
1,764
660
551
N1 comp192408_c0_seq1|m.4650 N2 comp174950_c0_seq1|m.10133
665
616 1,000
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500
2 N1
136
166
646
610 379
551 1,000
0 500
500 665
616 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Peroxiredoxin
N1 comp161327_c0_seq1|m.21473 N2 comp196746_c0_seq1|m.16621 N3 comp225147_c1_seq1|m.3590 16,000
0 8,000
16,000 8,000
0 8,000
16,000 8,000
0 8,000
16,000 8,000
3 2 N1
9,916
8,565
10,057
6,344 13,618
2,833 16,000
0 8,000
8,000 9,090
8,939
FPKM ChlH2O2RBw/o chl
Glutaredoxin
N1 comp197043_c0_seq1|m.26229 N2 comp196883_c0_seq1|m.24409 N3 comp221174_c0_seq1|m.16477 6,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
3 2 N1
497
367
1,012
489 6,721
1,297 6,000
0 3,000
3,000 439
335 6,000
6,000
6,000
FPKM ChlH2O2RBw/o chl
Contig Contig
Contig Contig
ND ND
753
726
0
3 2 N1
10,461
7,871
9,390
8,577 3,980
2,833 15,790
7,651
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0
3 2 N1
605
322
606
689 1,269
1,297 806
567
Green (rep. 2)w/o preyPaleGreen (rep. 1)
6,000 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000 6,000
0 3,000
3,000 6,000
6,000
6,000 16,000
8,000
16,000 8,000
0 8,000
16,000 8,000
0 8,000
16,000 8,000 16,000
0 8,000
8,000
1,000 500
1,000 500
0 500
1,000 500
0 500
1,000 500 1,000
0 500
500 6,000
3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
Glutathion S-transferase
N1 comp222120_c0_seq1|m.19841 N2 comp215852_c0_seq1|m.19804 N3 comp220161_c1_seq1|m.17653 N4 comp219327_c0_seq1|m.18450 N5 comp171992_c0_seq1|m.19016 N6 comp219524_c0_seq1|m.20621 20,000
0 10,000
500
0 250
20,000 10,000
500 250
0 250
500 250
0 250
250 22,249
9,211
2,479
2,058 10,423 500
0 250
250 14,538
9,818 0
10,000
20,000 10,000
0 10,000
20,000 10,000
0 10,000
10,000
FPKM ChlH2O2RBw/o chl
Oxidative stress responses 2
NDND
0
500
0 250
500 250
0 250
500 250
0 250
250 9,870
6,214
9,645
4,091 2,906 500
0 250
250 8,895
4,682
Green (rep. 2)w/o preyPaleGreen (rep. 1) ND
Thioredoxin
N1 comp222740_c10_seq1|m.26011 N2 comp215338_c0_seq1|m.23334 N3 comp218001_c0_seq1|m.3573 N4 comp217802_c0_seq1|m.12789 N5 comp214336_c0_seq1|m.23096 N6 comp223805_c0_seq1|m.9397 N7 comp212182_c0_seq1|m.21773 N8 comp229501_c0_seq1|m.21674 20,000
0 10,000
800
0 400
20,000 10,000
800 400
0 10,000
10,000
0 10,000
20,000 10,000
0 400
800 400
0 400
800 400 20,000
2
1 345678
N
8,010
3,904
9,518
4,547 22,858
3,408 20000
0 10,000
800
0 400
10,000 400
5,122
4,293 20,000
20,000
20,000
FPKM ChlH2O2RBw/o chl
Glutathione peroxidase
1,000
0 500
1,000 500
0 500
1,000 500
0 500
500 791
508
2,204
722 566 1,000
0 500
500 753
519 1,000
1,000
1,000
FPKM ChlH2O2RBw/o chl
Glutathione synthetase
400
0 200
400 200
0 200
400 200
0 200
400 200
N1
341236264135
400
0 200
200
3731
400
0 200
400 200
0 200
400 200
0 200
400 200
N1
12222462537335
400
0 200
200
2523
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
N1 comp170906_c0_seq1|m.12558
Contig Contig
0 800
0 400
800 400
0 400
800 400
0 400
800 400
2
1 345678
N
6,785
3,767
4,138
3,872 3,082
3,408 800
0 400
400
8,003
3,102
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0 593
253
859
441 993 1,292
505
Green (rep. 2)w/o preyPaleGreen (rep. 1)
20,000 10,000
20,000 10,000
0 10,000
20,000 10,000
0 10,000
20,000 10,000
0 10,000
10,000 1,000
500
1,000 500
0 500
1,000 500
0 500
500 1,000
0 500
500 1,000
1,000
1,000 20,000 10,000
20,000 10,000
0 10,000
10,000
0 10,000
20,000 10,000 20,000 20000
0 10,000
10,000 20,000
20,000
20,000
Oxidative stress responses 3
Carbonyl reductase
N1 comp222757_c0_seq1|m.17440 5,000
0 2,500
5,000 2,500
5,000
0 2,500
5,000 2,500
0 2,500
5,000 2,500
N1
844682,4866225016
0 2,500
2,500
71369
FPKM ChlH2O2RBw/o chl
Peptide methionine sulfoxide reductase
0
2 N1 2,949
468
563 1,783
284
N1 comp161358_c0_seq1|m.4904 N2 comp224705_c0_seq2|m.7781
4,292
4,232516 4,000
0 2,000
4,000 2,000
4,000
0 2,000
4,000 2,000
0 2,000
4,000 2,000
2 N1 2,056
410
144 924
284 0 2,000
2,000 1,652
415 4,845 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig
0
N1
1,0141041,119116311,81756
Green (rep. 2)w/o preyPaleGreen (rep. 1) 16
Apolipoprotein D
N1 comp222513_c0_seq1|m.20128 1,500
0 1,000
500
N1
29011,4726971
500
2300.9
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
FPKM ChlH2O2RBw/o chl
Contig
0
N1
2645229242517444
Green (rep. 2)w/o preyPaleGreen (rep. 1)
100
0 50
100 50
N1
7215681062453
N1 comp196062_c0_seq1|m.19674
150 150
10431
Cob(I)yrinic acid a,c-diamide adenosyltransferase
100
0 50
100 50
150 150
100 0 50
100 50
150 150
100
0 50
100 50
150 150
100
0 50
100 50
N1
5842166754653
150 150
8240
100
0 50
100 50
150 150
100 0 50
100 50
150 150
100
0 50
100 50
150 150 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig
1,500 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
1,500
0 1,000
500 500
1,500 1,000
4,000 2,000
4,000 2,000
4,000
0 2,000
4,000 2,000
0 2,000
4,000 2,000 0 2,000
2,000 5,000
2,500
5,000 2,500
5,000
0 2,500
5,000 2,500
0 2,500
5,000 2,500 0 2,500
2,500
Carotenoid synthesis
Carotene epsilon-monooxygenase
N1 comp221700_c0_seq1|m.16996 N2 comp225590_c0_seq1|m.8817 200
0 100
200 100
0 100
200 100
0 100
200 100
2 N1
131
184
212 152
168 200
0 100
100 153 192
FPKM ChlH2O2RBw/o chl
137
Phytoene desaturase
N1 comp217346_c0_seq1|m.11870 2,000
0 1,000
1,000
1,000 0 1,000 2,000
0 1,000
2,000 1,000
N1 54621,70755053
2,000
0 1,000
2,000 1,000
7340
FPKM ChlH2O2RBw/o chl
Geranylgeranyl
pyrophosphate synthase
300
0 150
300 150
0 150
300 150
0 150
150
1919131936
300
0 150
150
255155
300
0 150
300 150
0 150
300 150
0 150
150
175465133104
300
0 150
150
5948
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig
200
0 100
200 100
0 100
200 100
0 100
200 100
2 N1
99
113
86 188
168 200
0 100
100 151
204 58
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0
N1
5102658981,27837989
Green (rep. 2)w/o preyPaleGreen (rep. 1)
2,000 1,000
1,000
1,000 0 1,000 2,000
0 1,000
2,000 1,000 2,000
0 1,000
2,000 1,000
DNA repair
ALK B
N1 comp220611_c0_seq1|m.15695 80
0 40
80 40
N1 33 41 26 27 17 11
12 80 13
0 40
80 40
80
0 40
80 40
80
0 40
80 40
FPKM ChlH2O2RBw/o chl
Deoxyribodipyrimidine photo-lyase
1,000
0 500
500
N1
0.42900.0682105
N1 comp222533_c0_seq1|m.15479 1,000
0.8388
1,000
0 500
500 1,000 1,000
0 500
500 1,000 1,000
0 500
500 1,000
1,000
0 500
500
N1
0.411731,0290.0266
1,000
0.4310
1,000
0 500
500 1,000 1,000
0 500
500 1,000 1,000
0 500
500 1,000 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
DNA-(apurinic or apyrimidinic site) lyase
N1 comp225006_c0_seq1|m.7768 200
0 100
200 100
N1
73315550347
200
0 100
200 100
200
0 100
200 100
200
0 100
200 100
FPKM ChlH2O2RBw/o chl
MSH2
100
0 50
100 50
N1
182410112216
N1 comp225420_c0_seq1|m.4740
1925
0 50
100 50
0 50
100 50
0 50
100 50
100
0 50
100 50
N1
2125161493162828
0 50
100 50
0 50
100 50
0 50
100 50 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig Contig Contig
80
0 40
80 40
N1 33 30 10 9 10 11
16 80 21
0 40
80 40
80
0 40
80 40
80
0 40
80 40
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0
N1 7 51 3 28 5 29
10 81
Green (rep. 2)w/o preyPaleGreen (rep. 1)
XRCC
N1 comp221477_c2_seq1|m.17537 200
0 100
200 100
N1
51173615538273935
0 100
200 100
0 100
200 100
0 100
200 100
FPKM ChlH2O2RBw/o chl
Contig Contig
RAD51
N1 comp196015_c0_seq1|m.15894 500
0 250
500 250
N1
18386251649292928
500
0 250
500 250
500
0 250
500 250
500
0 250
500 250
FPKM ChlH2O2RBw/o chl
RAD5
80
0 40
80 40
N1
222219112317
N1 comp218612_c0_seq1|m.4221
3324
0 40
80 40
0 40
80 40
0 40
80 40
80
0 40
80 40
N1
4021362971172723
0 40
80 40
0 40
80 40
0 40
80 40 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig
500
0 250
500 250
N1 24
25
24
44 28
29 29
38 500
0 250
500 250
500
0 250
500 250
500
0 250
500 250
Green (rep. 2)w/o preyPaleGreen (rep. 1)
200
0 100
200 100
N1 51 57 27 16 11 24
18 13
0 100
200 100
0 100
200 100
0 100
200 100
Green (rep. 2)w/o preyPaleGreen (rep. 1)
200 100
200 100
200
0 100
200 100
200
0 100
200 100
200
0 100
200 100
190
Respiration 1
ATP/ADP translocase
N1 comp196908_c0_seq1|m.19210 N2 comp222692_c0_seq1|m.11667 2,000
0 1,000
100
0 50
2,000 1,000
100 50
0 50
100 50
0 50
100 50
1 2
N
1,1474635771,7281,135
100
0 50
50
1,6061,474
0 1,000
2,000 1,000
0 1,000
2,000 1,000
0 1,000
2,000 1,000
636
FPKM ChlH2O2RBw/o chl
cox15
N1
1498171941912511131
500
0 250
500 250
0 250
500 250
0 250
500 250 500
0 250
250
N1
1417174871910415181
500
0 250
500 250
0 250
500 250
0 250
500 250 500
0 250
250 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
N1 comp228272_c0_seq1|m.12304
60
0 30
60 30
N1
295043422920
N1 comp169334_c0_seq1|m.12493
2921
0 30
60 30
0 30
60 30
0 30
60 30
cox19
60
0 30
60 30
N1
294016811162219
0 30
60 30
0 30
60 30
0 30
60 30 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Prohibitin 1
300
0 150
300 150
1092742296172197
300
0 150
300 150
300
0 150
300 150
300
0 150
150
300
0 150
300 150
2138331064706767
300
0 150
300 150
300
0 150
300 150
300
0 150
150 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Prohibitin 2
200
0 100
200 100
5394599911570257
0 100
200 100
0 100
200 100
0 100
100
200
0 100
200 100
86365711003278285
0 100
200 100
0 100
200 100
0 100
100 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
TIM14
0 100 50
100 50
71232017413390
0 100 50
100 50
0 100 50
100 50
0 100 50
50
0 100 50
100 50
11314706161817
0 100 50
100 50
0 100 50
100 50
0 100 50
50 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig Contig
0 100
0 50
100 50
0 50
100 50
0 50
100 50
1 2
N
1,1471,1221,076798807
100
0 50
50
7186351,054
Green (rep. 2)w/o preyPaleGreen (rep. 1) 115
TIM17
30
0 15
30 15
15714621422
30
0 15
30 15
30
0 15
30 15
30
0 15
15 30
0 15
30 15
30528
30
0 15
30 15
30
0 15
30 15
30
0 15
15 Green (rep. 2)w/o preyWhiteFPKM Green (rep. 1) ChlH2O2RBw/o chl NDND 2,000
1,000
2,000 1,000
0 1,000
2,000 1,000
0 1,000
2,000 1,000
0 1,000
2,000 1,000
Respiration 2
TIM44
80
0 40
50 40
0 40
80 40
0 40
80 40
N1
394518131424
N1 comp182943_c0_seq1|m.12522 80
0 40
80 40
2757
80
0 40
50 40
0 40
80 40
0 40
80 40
N1 397340762416 80
0 40
80 40
2522
Green (rep. 2)w/o preyWhiteFPKM Green (rep. 1) ChlH2O2RBw/o chl
TIM50
200
0 100
200 100
2 N1
132 14674 68 110
108 N1 comp168559_c0_seq1|m.14233 N2 comp221198_c0_seq1|m.14508
103 200 194
0 100
200 100 200
0 100
200 100 200
0 100
200 100
200
0 100
200 100
2 N1
132 148355 264 104 172
110 200 134
0 100
200 100 200
0 100
200 100 200
0 100
200 100 Green (rep. 2)w/o preyWhiteFPKM Green (rep. 1) ChlH2O2RBw/o chl
TOM40
100 0 50
100 50
N1
113114101746078
N1 comp227996_c0_seq1|m.16805 150
150
67109
100 0 50
100 50 150
150 100 0 50
100 50 150
150 100 0 50
100 50 150
150
100 0 50
100 50
N1
1131341031636945
150
150
6462
100 0 50
100 50 150
150 100 0 50
100 50 150
150 100 0 50
100 50 150
150 Green (rep. 2)w/o preyWhiteFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig Contig
v-ATPase subunit A
0
2 N1
288 902 986 597
316 709
N1 comp227542_c0_seq1|m.10798 N2 comp221051_c0_seq1|m.7823
351 609
1,000
0 500
1,000 500
2 N1
288 246 284 673
294 1,412
705 1,000 711
0 500
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
v-ATPase subunit B
N1 comp196952_c0_seq1|m.13622 0 1,000 500
1,000 500
0 1,000 500
1,000 500
0 1,000 500
1,000 500
N1
258248404739416307
0 1,000 500
1,000 500
428344
FPKM ChlH2O2RBw/o chl
v-ATPase subunit C
2,000
0 1,000
2,000 1,000
2 N1
1942572082583122,772 304349 2,000
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000
FPKM ChlH2O2RBw/o chl
N1 comp196930_c0_seq1|m.11356 N2 comp196942_c0_seq1|m.21462
v-ATPase subunit D
N1 comp196607_c0_seq1|m.18535 0 600 300
600 300
N1 266253393560339474288335 0 300
600 300
0 300
600 300
0 300
600 300
FPKM ChlH2O2RBw/o chl
v-ATPase subunit E
500
0 250
500 250
0 250
500 250
0 250
250
308453305222346
500
0 250
250
269343
500
0 250
500 250
0 250
500 250
0 250
250
251167232265264
500
0 250
250
241165
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
v-ATPase subunit F
600
0 300
600 300
600
0 300
600 300
600
0 300
300
490281211144154
600
0 300
600 300
141119
FPKM ChlH2O2RBw/o chl
v-ATPase subunit H
150
0 100 50
100 50
105104
150
149156
150
0 100 50
100 50
150 150
0 100 50
100 50
150 150
0 100 50 50
151126133 150
0 100 50
100 50
123132
150
14090
150
0 100 50
100 50
150 150
0 100 50
100 50
150 150
0 100 50 50
9694115
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Vacuolar-type H+-ATPase
217
V-ATPase subunit c’’
800
0 400
400
109291368149223
800
106
800
0 400
400 800 800
0 400
400 800 800
0 400
400
814800
0 400
400
115108185374366
800
385
800
0 400
400 800 800
0 400
400 800 800
0 400
400 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Contig Contig Contig Contig
0 500
500
0 500
500
0 500
500
N1
3022485526491054872
0 500
500
442692
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0
2 N1
194 203 252 362 170 202
344 805
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0 600 300
600 300
N1
266262335329181271233340
0 300
600 300
0 300
600 300
0 300
600 300
Green (rep. 2)w/o preyPaleGreen (rep. 1)
600
0 300
600 300
600
0 300
600 300
600
0 300
300
394642309217327
600
0 300
600 300
188296
Green (rep. 2)w/o preyPaleGreen (rep. 1)
2,000 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000
2,000
0 1,000
2,000 1,000 1,000
1,000
1,000
1,000 1,000
1,000 1,000
1,000 1,000
500
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
1,000
0 500
1,000 500
Proteolysis 1
Cathepsin A
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) 2,000
0 1,000
2,000 1,000
1,000
0
2,000 1,000
1,000
0
2,000 1,000
4 3 2 N1
301 330 1,058 1,772 687
1,202 N1 comp216944_c0_seq1|m.12834
N2 comp217123_c0_seq1|m.13270 N3 comp217838_c0_seq1|m.13398 N4 comp221953_c0_seq1|m.12720
1,000
0
2,000 1,000
434 990
2,000
0 1,000
2,000 1,000
1,000
0
2,000 1,000
1,000
0
2,000 1,000
4 3 2 N1
301 522 433 427 565 2,839
1,000
0
2,000 1,000
529 569 ChlH2O2RBw/o chl
Cathepsin C
FPKM
N1 comp214966_c0_seq1|m.12794 N2 comp221851_c2_seq3|m.12596
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
2 N1 1,950
1,011
670
637 590
432 1,500
0 1,000 500
1,500 1,000 500
1,059
1,011 ChlH2O2RBw/o chl
Cathepsin F
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) 300
0 150
300 150
N1
18316210681
N1 comp221740_c0_seq1|m.7856
142134
0 150
300 150
0 150
300 150
0 150
300 150
229255
300
0 150
300 150
N1
16312781136171
0 150
300 150
0 150
300 150
0 150
300 150
119131
ChlH2O2RBw/o chl 166
Cathepsin B
FPKM
N1 comp222264_c1_seq2|m.24062 N2 comp222264_c0_seq2|m.18254 N3 comp161120_c0_seq1|m.21113 N4 comp196690_c1_seq1|m.20318 N5 comp196690_c0_seq1|m.25763 N6 comp161120_c1_seq1|m.24792 N7 comp222291_c0_seq1|m.19331 N8 comp219614_c1_seq1|m.18120 N9 comp224223_c0_seq1|m.11597 20,000
0 10,000
0
2,000 100
0 50 1,000
20,000 10,000
20,000
0 10,000
20,000 10,000
20,000
0 10,000
20,000 10,000
2,000
1,000 50
2
1 34567 89
N
37,86533,0039,89710,4227,13814,147
20,000
0 10,000
100
20,000 10,000
30,13630,023
0 2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
100
0 50
50 100 100
0 50
50 100 100
0 50
50 100 ChlH2O2RBw/o chl
Contig Contig Contig
Contig
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
1,500
0 1,000 500
1,500 1,000 500
2 N1 1,177
1,162
2,029
1,513 508
432 1,500
0 1,000 500
1,500 1,000 500
1,332
712
Green (rep. 2)w/o preyPaleGreen (rep. 1)
0 0
100
0 50
50
2
1 34567 89
N
37,90934,78953,44437,55311,73914,147
100
21,95114,048
100
0 50
50 100 100
0 50
50 100 100
0 50
50 100
Green (rep. 2)w/o preyPaleGreen (rep. 1)
20,000 10,000
20,000 10,000
20,000
0 10,000
20,000 10,000
20,000
0 10,000
20,000 10,000 20,000
0 10,000
20,000 10,000
2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
0 2,000 1,000
2,000 1,000
Cathepsin L
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) 6,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000 6,000
6,000
3 2 N1
3,413
6,525
4,023 1,694
1,671
3,740 N1 comp227258_c0_seq1|m.16318
N2 comp196035_c1_seq1|m.18909 N3 comp217656_c0_seq1|m.16225
6,000
0 3,000
3,000 2,176 3,038
6,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000
0 3,000
6,000 3,000 6,000
6,000
3 2 N1
3,713
1,888
1,479 1,263
1,671 5,617
6,000
0 3,000
3,000 3,652 3,638 ChlH2O2RBw/o chl
6,000 6,000
Contig
Proteolysis 2
Cathepsin Z
N1 comp171747_c0_seq1|m.20352 N2 comp212828_c0_seq1|m.20688 N3 comp214909_c0_seq1|m.27463 N4 comp214909_c1_seq2|m.21648 800
0 400
800 400
0 400
400 800
0 400
800 400
4 3 2 N1
1,048
992
581
713 487
867 800
0 400
400 853
934
FPKM ChlH2O2RBw/o chl
Chymotrypsin
N1 comp227093_c0_seq1|m.4050 N2 comp224595_c1_seq1|m.18363 N3 comp224121_c0_seq1|m.5208 500
0 250
250 185
155
489
171 161 235
159 500
0 250
250 500
0 250
250 500
0 250
250
FPKM ChlH2O2RBw/o chl
Contig
NDND ND
800
0 400
800 400
0 400
400 800
0 400
800 400
4 3 2 N1
1,100
1,133
1,803
1,709 756
867 800
0 400
400 976
1,035
Green (rep. 2)w/o preyPaleGreen (rep. 1)
500
0 250
250 500
0 250
250 500
0 250
250 500
0 250
250 Green (rep. 2)w/o preyPaleGreen (rep. 1) NDND NDND
188
279
55
15 309 169
81
Methylsterol monooxygenase
N1 comp228408_c0_seq1|m.17822 N2 comp224022_c0_seq1|m.7534 N3 comp228514_c0_seq1|m.11837 N4 comp218051_c0_seq1|m.11145 200
0 100
200 100
4 3 2 N1
260
326
226
142 122
152 361
350 0 100
200 100
0 100
200 100
0 100
200 100
FPKM ChlH2O2RBw/o chl
Squalene monooxygenase
1,000
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500
2 N1
1,0048216550438
N1 comp216080_c1_seq1|m.5734 N2 comp216080_c0_seq1|m.19550
1,684
1,000
0 500
500
751,236
1,000
0 500
1,000 500
0 500
1,000 500
0 500
1,000 500
2 N1
680
175
31 97
38 866 1,000
0 500
500 167 963 Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
L-gulonolactone oxidase
80
0 40
80 40
0 40
80 40
0 40
80 40
N1
3744810413
N1 comp220489_c0_seq1|m.13475 80
0 40
40
478
80
0 40
80 40
0 40
80 40
0 40
80 40
N1
683403463
80
0 40
40
252
Green (rep. 2)w/o preyPaleFPKM Green (rep. 1) ChlH2O2RBw/o chl
Oxygen reducing metabolism
ND
Contig Contig
Contig
200
0 100
200 100
4 3 2 N1 0 100
200 100
0 100
200 100
0 100
200 100
Green (rep. 2)w/o preyPaleGreen (rep. 1)
132
90
156
160 192
152 272
199
Myosin
Type I
N1 comp221724_c0_seq1|m.7380 N2 comp228109_c0_seq1|m.3268 N3 comp222815_c1_seq1|m.8438 300
0 150
300 150
300
0 150
300 150
300
0 150
300 150
3 2 N1
121
416
175
421 118
366 300
0 150
300 150
307
451
FPKM ChlH2O2RBw/o chl
Type II
N1 comp226013_c0_seq2|m.5781 N2 comp152034_c0_seq1|m.18471 200
0 100
200 100
0 100
200 100
0 100
200 100
2 N1
40
115 41
104 50
204 200
0 100
200 100
99 110
FPKM ChlH2O2RBw/o chl
Other types
300
0 150
150
381727920254
300
229159
0 150
150 300
0 150
150 300
0 150
150
FPKM ChlH2O2RBw/o chl
Contig Contig
300
0 150
300 150
300
0 150
300 150
300
0 150
300 150
3 2 N1 300
0 150
300 150
Green (rep. 2)w/o preyPaleGreen (rep. 1)
91
349
275
442 390
366 132
404
200
0 100
200 100
0 100
200 100
0 100
200 100
2 N1 200
0 100
200 100
Green (rep. 2)w/o preyPaleGreen (rep. 1)
27
66 149
188 227
204 14 154
300
0 150
150 300
0 150
150 300
0 150
150 300
0 150
150 Green (rep. 2)w/o preyPaleGreen (rep. 1) 1446341471130157