Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion
during chrysanthemum cross breeding
Fengjiao Zhang, Zhiquan Wang, Wen Dong, Chunqing Sun, Haibin Wang, Aiping Song,
Lizhong He, Weimin Fang, Fadi Chen, Nianjun Teng
Supplementary Information
Supplementary Table S1. The 129 KEGG pathways.
Supplementary Table S2 Differential expression genes in normal (NE12) and abortive
(AE18) chrysanthemum embryos.
Supplementary Table S3 Differential expression genes in normal (NE18) and abortive
(AE18) chrysanthemum embryos.
Supplementary Table S4. Differentially expressed genes in normal and abortive
chrysanthemum embryos.
Supplementary Table S5. Primer sequences for qRT-PCR.
Supplementary Fig. S1. Clusters of orthologous groups (COG) function classification of
chrysanthemum embryo transcriptome. The 25,297 sequences were grouped into 25
categories.
Supplementary Fig. S2. Gene Ontology (GO) classifications of chrysanthemum embryo
transcriptome. The transcriptome datasets are grouped into three categories: biological
process, cellular component and molecular function.
Supplementary Fig. S3. Differentially expressed genes among transcriptome datasets.
The number of up- (a) and down-regulated (b) genes between AE18 and NE12, AE18
and NE18 are summarised. Complete information for each gene list can be found in
Tables S2 & S3. (All Venn diagrams produced by Venny28).
Supplementary Fig. S4. The workflow for transcriptomic analysis of chrysanthemum
embryos.
Supplementary Fig. S5. The workflow for proteomic analysis of chrysanthemum
embryos.
Fig. S1 Clusters of orthologous groups (COG) function classification of chrysanthemum embryo
transcriptome
Fig. S2 Gene Ontology (GO) classifications of chrysanthemum embryo transcriptome
Fig. S3 Differentially expressed genes among transcriptome datasets
Fig. S4 The workflow for transcriptomic analysis of chrysanthemum embryos
Fig. S5 The workflow for proteomic analysis of chrysanthemum embryos
Table S4. Differential expression genes in normal and abortive chrysanthemum embryos
Genes ID
Cell senescence and death
CL8107.Contig2_All
CL3742.Contig7_All
CL8052.Contig3_All
Unigene23480_All
Unigene31215_All
CL7004.Contig3_All
CL15915.Contig2_All
Unigene29849_All
Unigene31333_All
Unigene49135_All
Unigene51752_All
Unigene7475_All
Unigene13579_All
Unigene5306_All
Unigene2161_All
Unigene21484_All
Unigene21604_All
Unigene28134_All
Unigene15193_All
CL377.Contig5_All
Reactive oxygen species scavenger
CL5385.Contig1_All
Unigene9496_All
CL15040.Contig1_All
CL8422.Contig3_All
Unigene18167_All
Unigene21550_All
Unigene24749_All
CL14312.Contig1_All
CL5541.Contig6_All
NE12 FPKM
NE18 FPKM
AE18 FPKM
Nr-annotation
3.08
4.30
5.59
10.90
14.52
28.83
2.43
2.75
4.76
0.60
2.33
27.77
1.62
27.71
172.46
358.29
897.17
216.31
252.15
2.7297
8.14
14.12
31.27
34.67
80.55
44.84
5.75
7.91
10.74
2.74
7.56
13.75
5.03
8.05
372.90
179.01
373.90
84.84
119.81
0.5347
17.74
13.10
22.69
27.68
68.14
59.78
5.54
7.39
3.67
1.86
0.51
14.22
4.43
30.56
345.67
230.74
470.00
105.20
138.58
2.8369
senescence-associated protein
senescence-related protein
senescence-related protein
serine/threonine-protein kinase CTR1-like
serine/threonine-protein kinase WNK11-like
caspase, putative
caspase, putative
aspartic proteinase nepenthesin-2-like
aspartic proteinase nepenthesin-1 precursor, putative
lethal leaf spot 1-like protein
aspartic proteinase
apoptosis-inducing factor homolog A-like
Cytochrome c
Cytochrome c
Cytochrome c
cysteine protease
cysteine protease
cysteine proteinase
cysteine protease
pathogenesis-related protein
0.42
2.23
4.18
11.01
20.62
2207.19
31.02
8.98
1.96
1.80
4.37
13.24
37.54
51.72
925.02
134.32
62.48
8.30
1.91
7.37
16.11
38.27
44.56
1124.31
118.13
51.58
6.25
peroxidase
peroxidase
peroxidase
peroxidase
peroxidase 31-like
catalase
ascorbate oxidase
L-ascorbate oxidase homolog
L-ascorbate oxidase homolog
Unigene7903_All
CL11780.Contig1_All
CL6269.Contig1_All
Unigene12018_All
Phytohormone signaling
Unigene29518_All
Unigene29521_All
Unigene40598_All
CL3066.Contig5_All
CL12550.Contig2_All
Unigene3750_All
Unigene2545_All
Unigene31648_All
CL3106.Contig4_All
Unigene23347_All
Unigene26909_All
Unigene10574_All
Unigene10399_All
Unigene25739_All
Unigene587_All
Unigene22446_All
Cell division and expansion
Unigene24705_All
Unigene14594_All
Unigene8344_All
Unigene27839_All
CL5976.Contig2_All
Unigene11714_All
CL3367.Contig4_All
CL9620.Contig1_All
CL9217.Contig2_All
Cytoskeleton
Unigene37701_All
0.99
41.35
150.59
9.23
1.73
20.07
544.16
4.31
3.75
23.34
406.46
4.73
glutathione peroxidase
glutathione peroxidase 2
glutathione peroxidase 2
dehydroascorbate reductase
2.55
2.70
6.81
1.52
15.94
12.30
5.83
10.89
6.23
3.09
12.89
64.01
94.63
2.91
11.03
5.97
1.06
1.35
1.43
0.17
6.72
10.04
9.63
44.12
32.48
19.44
30.38
20.43
191.69
7.79
59.41
1.31
0.99
0.96
0.46
0.05
6.80
3.82
13.31
1.51
24.57
15.62
26.33
25.46
240.30
12.06
48.09
1.11
auxin-induced protein
auxin-induced protein
auxin response factor 4-like
auxin response factor, putative
auxin response factor, putative
auxin-induced protein 5NG4, putative
gibberellin-regulated family protein
gibberellin 20-oxidase No3
gibberellin 2-oxidase No1
gibberellin 2-oxidase
gibberellin 2-oxidase
ethylene responsive element binding protein C4
ethylene responsive element binding protein C1
ethylene-responsive transciptional coactivator-like protein
ethylene-responsive factor-like protein 1
ethylene insensitive protein, putative
42.2137
23.3011
11.47
9.40
7.08
36.41
15.05
1.21
7.72
16.0515
5.0287
2.66
58.64
29.64
15.58
30.47
0.79
21.09
13.8934
5.7835
3.04
25.87
1.01
34.21
16.83
3.80
18.81
expansin
putative expansin
alpha-expansin 11 precursor, putative
extensin-like protein
beta expansin 2 precursor
Histone 3
Histone H3
Histone H3
Histone H2AX-like
6.39
0.58
0.09
cytoskeletal protein
Unigene35314_All
Unigene48753_All
Unigene3079_All
Unigene22260_All
Unigene48739_All
Unigene31578_All
Unigene8380_All
Energy metabolism
Unigene38257_All
Unigene43190_All
Unigene43385_All
CL3950.Contig10_All
Unigene34992_All
CL5835.Contig1_All
CL14726.Contig2_All
CL12522.Contig1_All
CL862.Contig2_All
Unigene51682_All
CL11733.Contig2_All
Unigene15994_All
CL3082.Contig5_All
Unigene13910_All
CL9471.Contig1_All
Unigene8208_All
CL7696.Contig7_All
CL4695.Contig1_All
Unigene3738_All
Unigene55850_All
Protein synthesis
Unigene26963_All
Unigene25222_All
Unigene13976_All
Unigene20511_All
9.49
6.51
1.36
7.12
8.34
15.46
34.02
0.20
2.59
0.18
1.71
29.45
4.18
10.04
0.28
2.97
0.75
3.31
7.34
3.38
16.73
Guillardia theta ACT1 gene for actin 1
actin related protein
actin related protein
actin
actin
cytoplasmic dynein light chain, putative
tubulin beta chain, putative
17.63
5.54
4.01
2.62
4.88
4.88
6.28
2.90
0.50
0.00
1.9832
0.14
43.65
13.59
19.39
11.11
1.65
4.40
11.11
7.51
0.34
0.00
0.00
0.85
1.76
1.65
3.15
5.03
1.57
4.16
1.5665
7.51
22.88
56.12
44.60
29.01
7.09
32.90
35.92
27.16
0.28
0.00
0.00
0.77
1.23
5.36
2.66
7.04
0.98
0.19
0.9369
4.92
21.70
37.28
55.25
38.12
8.20
33.64
34.31
26.72
ATP synthase subunit alpha
ATPase subunit 6
ATPase subunit 9
plasma membrane H+ ATPase
plasma membrane H+ ATPase
aconitate hydratase, mitochondrial
UDP-glucose 4-epimerase
UDP-glucose crocetin glucosyltransferase
pyruvate kinase, cytosolic isozyme-like
pyruvate kinase
pyruvate kinase
2-succinylbenzoate-CoA ligase
phosphoenolpyruvate carboxykinase
vacuolar proton translocating ATPase 100 kDa subunit
phospholipid-transporting ATPase 1-like
phospholipid-translocating P-type ATPase flippase family protein
type IIB calcium ATPase MCA5
calcium-transporting ATPase 12, plasma membrane-type-like
calcium-transporting ATPase 12, plasma membrane-type-like
calcium-transporting ATPase 12, plasma membrane-type-like
9.99
7.32
17.61
2.41
40.12
29.72
54.00
17.57
4.62
1.58
6.92
1.57
late embryogenesis abundant protein group 9 protein
late embryogenesis abundant protein-like
late embryogenesis abundant protein
vegetative cell wall protein gp1 precursor, putative
Unigene27790_All
Unigene51655_All
Unigene48142_All
Unigene48132_All
Unigene50970_All
Unigene29371_All
Unigene8353_All
Unigene31550_All
Unigene7450_All
CL11305.Contig3_All
CL15810.Contig2_All
CL2190.Contig10_All
Proteolysis
Unigene10512_All
Unigene952_All
Unigene14006_All
Unigene26883_All
Unigene30058_All
CL12798.Contig1_All
Unigene29903_All
Unigene24730_All
Unigene21775_All
Unigene17203_All
DNA processing
Unigene22054_All
Unigene36576_All
Unigene13401_All
Unigene16330_All
Unigene43204_All
Unigene14000_All
Unigene13706_All
Transcription factor
Unigene5325_All
4.94
0.79
0.55
0.20
0.86
23.96
165.21
66.82
13.06
18.32
12.58
0.1795
13.93
20.44
9.67
3.84
21.44
4.21
533.72
134.53
3.75
55.32
42.19
0.1318
1.49
0.42
0.21
0.00
0.00
12.48
485.89
170.96
13.62
56.58
41.43
0.0424
transcription activator-related protein
ubiquitin-60S ribosomal protein L40
60S ribosomal protein L12
ribosomal protein S28e
ribosomal protein S28e
ran-type small G protein
calcium-binding protein
probable calcium-binding protein CML27-like
probable calcium-binding protein CML31
calmodulin-related protein isoform 4
calmodulin-related protein isoform 4
eukaryotic initiation factor 4A
8.25
30.18
7.00
5.05
4.88
5.91
14.00
14.80
6.21
2.48
3.72
13.44
2.07
1.89
1.72
2.08
7.45
4.89
1.69
5.40
4.62
16.61
4.98
2.60
3.23
3.07
6.50
7.41
7.06
5.74
ubiquitin
ubiquitin
proteasome component (PCI) domain protein
26S proteasome subunit P45
20S proteasome beta subunit, type 4
proteasome subunit beta type
ubiquitin-protein ligase, putative
ubiquitin-conjugating enzyme
probable ubiquitin-conjugating enzyme E2
E3 ubiquitin-protein ligase Os04g0590900-like
3.16
3.64
5.23
6.35
4.86
7.19
7.07
0.00
0.47
4.13
1.93
1.02
4.62
3.59
1.66
1.20
2.55
3.31
2.30
2.90
2.04
DNA replication licensing factor MCM7, putative
alkylated DNA repair protein alkB homolog 8
DNA replication licensing factor MCM3-like protein
DNA repair helicase XPB1-like
ribonucleoside-diphosphate reductase
cyclic nucleotide-gated ion channel 5-like,probable
cyclic nucleotide-gated ion channel 4-like
1.62
130.34
70.59
AP2/ERF domain-containing transcription factor
Unigene7146_All
Unigene26661_All
Unigene14020_All
Unigene1985_All
Unigene14870_All
Unigene23338_All
Unigene21429_All
Unigene422_All
Unigene50055_All
Unigene8269_All
Unigene12981_All
Unigene29016_All
Unigene41061_All
Unigene50638_All
Unigene24815_All
Unigene13275_All
Unigene26736_All
Unigene5088_All
Unigene15074_All
Unigene18144_All
Unigene27265_All
Unigene31404_All
Unigene23825_All
110.35
4.53
5.08
10.11
4.50
13.84
29.11
6.47
3.56
21.92
18.04
12.52
7.64
1.58
103.61
9.30
9.68
51.55
42.81
5.64
7.26
1.69
9.53
39.64
9.42
54.59
113.12
74.82
60.80
10.84
6.88
23.22
5.52
1.27
1.42
1.19
6.04
28.97
4.14
2.44
29.94
167.31
13.24
16.51
26.47
10.01
48.63
12.19
29.50
87.48
54.32
43.44
27.22
15.10
13.89
12.16
2.46
2.22
1.41
0.45
80.38
4.30
3.89
69.26
183.23
14.94
16.16
28.27
22.84
AP2/ERF transcription factor
AP2/ERF domain-containing transcription factor
WRKY transcription factor 22
probable WRKY transcription factor 48
probable WRKY transcription factor 48
WRKY transcription factor 2
WRKY transcription factor 1
WRKY transcription factor, putative
putative MYB transcription factor
r2r3-myb transcription factor, putative
zinc finger protein, putative
zinc finger protein 2-like
zinc finger protein CONSTANS-LIKE 16
zinc finger protein, putative
leucine-rich repeat-containing protein, putative
Leucine-rich repeat receptor protein kinase EXS precursor, putative
Leucine-rich repeat receptor protein kinase EXS precursor, putative
ethylene-responsive transcription factor 2-like
ethylene-responsive transcription factor 4-like
ethylene-responsive transcription factor ERF061-like
ethylene-responsive transcription factor ERF012-like
ethylene-responsive transcription factor CRF4
ethylene-responsive transcription factor, putative
All genes in this list have a P-value for differential expression smaller than 10-5. FPKM (Fragments Per kb per Million fragments)
NE12: Normal embryos at 12 days after pollination; NE18: Normal embryos at 18 days after pollination; AE18: Abortive embryos at 18 days after pollination.
Table S5. Primer sequences for qRT-PCR
Unigene
Forward primer
Reverse primer
CL15915.Contig2_All caspase
ATACATCGGCTTTCACAGGC
ACAAAACGGCCTACCACTTG
CL8107.Contig2_All senescence-associated protein
TGGCACCTCTAGCCTCAAAT
GGGGACTCATGGAGAACAGA
CL5976.Contig2_All beta expansin 2 precursor
AAAGAGGAAAATAGCGACGAGTG
GCGACTAGAACCTGTTGGGAGTAT
Unigene37701_All cytoskeletal protein
TTCCCTACCCAGTCAGCGTG
ACGGGACAGGTTTGTTCACAG
Unigene34992_All plasma membrane H+ ATPase
CTTGCATCGTGGGAATTCTT
TGTGCCATTTTCCACTTTCA
Unigene13706_All cyclic nucleotide-gated ion channel 4-like
CACGGGCTTGTTTATTGACC
CACTCAAACTGCAGCCACAT
Unigene31648_All gibberellin 20-oxidase No3
AATGGACAAAGTCGTGAGGC
AACTCGAGGAAAGCAGACCA
Unigene25739_All ethylene-responsive transciptional
ATGGGTGCAATGTCACAAGA
CTTCCTAGCGTAAACAGCGG
GCCTATGCATTAAGGGGTCA
TCTTCCATTGTTTTCCCTCG
GCTGAGGACTCCAGCATCAT
TTTGCCAGCGTTGTTTACTG
Unigene25222_All late embryogenesis abundant protein-like
TGACAACTGGTGGTATGGAAGG
TGACTGTTACTTTCGTCGTGGC
Unigene7903_All glutathione peroxidase
AACAAGCTCAACGGCAAAGT
AAACTGGTTGCATGGAAAGC
Unigene26736_All Leucine-rich repeat receptor protein kinase
AAGTCATATCACTTTCAATACCAAACAC
CGAATTTGACGACAAGTCTAGCAG
CGCAAGAAAACACGTTGAAA
AAATTATGGTTGCCGACGAG
coactivator-like protein
Unigene23825_All ethylene-responsive transcription factor,
putative
Unigene14006_All proteasome component (PCI) domain
protein
EXS precursor, putative
Unigene23338_All WRKY transcription factor 2