Download Figure S1 GO enrichment analysis for genes in expression pattern 1

0
1
-lg(P-value)
2
3
4
G-protein coupled receptor signaling pathway
ion transport
multicellular organismal development
Wnt receptor signaling pathway
protein homooligomerization
oxygen transport
dicarboxylic acid transport
potassium ion transport
homophilic cell adhesion
adherens junction assembly
photosynthesis
adenylate cyclase-modulating G-protein
coupled receptor signaling pathway
Figure S1 GO enrichment analysis for genes in expression pattern 1
5
0
-lg(P-value)
2
4
catecholamine
biosynthetic process
aromatic amino acid
family metabolic
process
Figure S2 GO enrichment analysis for genes in expression pattern 2
0
2
-lg(P-value)
4
6
8
10
12
metabolic process
oxidation-reduction process
transmembrane transport
proteolysis
regulation of catalytic activity
aromatic amino acid family metabolic process
'de novo' IMP biosynthetic process
transport
carbohydrate metabolic process
L-serine biosynthetic process
cellular carbohydrate metabolic process
proline biosynthetic process
pentose-phosphate shunt
phototransduction
visual perception
nucleoside metabolic process
nucleotide catabolic process
lipid metabolic process
cellular amino acid metabolic process
sulfate transport
Figure S3 GO enrichment analysis for genes in expression pattern 3 (the top
20 enriched terms were showed)
0
0.5
-lg(P-value)
1
1.5
2
nucleosome assembly
reciprocal meiotic recombination
DNA catabolic process,
endonucleolytic
chitin metabolic process
Figure S4 GO enrichment analysis for genes in expression pattern 4
0
1
-lg(P-value)
2
3
4
microtubule-based movement
glycolysis
glycerol metabolic process
positive regulation of apoptotic process
inositol catabolic process
protein metabolic process
tricarboxylic acid cycle
regulation of microtubule polymerization
or depolymerization
Figure S5 GO enrichment analysis for genes in expression pattern 5
0
1
2
-lg(P-value)
3
4
5
6
protein metabolic process
protein polymerization
microtubule-based process
glycolysis
negative regulation of biosynthetic process
tyrosine metabolic process
GTP catabolic process
proteolysis
cellular amino acid metabolic process
negative regulation of nucleotide metabolic
process
cell motility
intraflagellar transport
L-phenylalanine catabolic process
protein targeting
Figure S6 GO enrichment analysis for genes in expression pattern 6
7
8
0
5
-lg(P-value)
10
15
20
chitin metabolic process
homophilic cell adhesion
chitin catabolic process
response to oxidative stress
alcohol metabolic process
proteolysis
multicellular organismal development
oxidation-reduction process
microtubule-based process
carbohydrate metabolic process
regulation of transcription, DNA-dependent
dicarboxylic acid transport
steroid hormone mediated signaling pathway
protein polymerization
Wnt receptor signaling pathway
tetrahydrofolate biosynthetic process
sphingomyelin catabolic process
neurotransmitter secretion
negative regulation of cell differentiation
ecdysis, chitin-based cuticle
Figure S7 GO enrichment analysis for genes in expression pattern 7
25
0
1
2
-lg(P-value)
3
4
5
6
7
lipid transport
DNA repair
cell-cell signaling
microtubule-based movement
histidine catabolic process to glutamate and formamide
cysteinyl-tRNA aminoacylation
proteolysis
base-excision repair
rRNA processing
intracellular signal transduction
signal transduction
oxidation-reduction process
response to stress
metal ion transport
phosphate ion transport
transcription from RNA polymerase III promoter
poly(A)+ mRNA export from nucleus
mitotic spindle assembly checkpoint
nucleus-associated proteasomal ubiquitin-dependent…
C-5 methylation of cytosine
Figure S8 GO enrichment analysis for genes in expression pattern 8 (the top
20 enriched terms were showed)
Table S1 Transcriptome sequencing data statistics
Sample
Total Reads (M)
Total Base (Gb)
mb
40.71
5.09
1in
82.21
10.28
2in
71.09
8.89
3in
90.57
11.32
4in
86.93
10.87
5in
74.55
9.32
5d
80.01
10.00
10d
77.85
9.73
st
Abbreviation: Embryo (emb), the 1 instar nymph (1in), the 2nd instar nymph (2in),
the 3rd instar nymph (3in), the 4th instar nymph (4in), the 5th instar nymph (5in), the
5-day adult (5d) and 10-day adult (10d).
Table S2 Estimation of S. furcifera genome size using K-mer analysis
K
Kmer num
Genome size(bp) Used reads
Used bases
Peak
17
67
49,287,456,386
735,633,677
467,361,061
56,765,233,362
Table S3 The alignment information of short reads mapping to the genome
Reads
Genome
Average sequencing depth (X)
64.34
Mapping rate (%)
95.73
Coverage (%)
99.51
Coverage at least 4X (%)
98.34
Coverage at least 10X (%)
95.55
Coverage at least 15X (%)
91.94
1
Table S4 The RNA-seq datasets used to in this study
RNA-seq
RNA-seq (MDS )
RNA-seq
Resource
This study
NCBI
Accession
This study
SRP009194
Gi:74252047EST data
NCBI
74252202
Notes: MDS: Multiple developmental stages, the EST data was downloaded from
NCBI Genbank database (gi74252047--gi74252202).
2
Table S5 Assessment of genome coverage by assembled transcripts of S. furcifera
Unigene
Dataset
Number
Total length
(bp)
Covered by
Assembly (%)
With >90% sequence in
one scaffold
With >50% sequence in
one scaffold
Number
%
Number
%
>0bp
34,101
34,978,097
94.68
29,859
87.56
33,665
98.72
>200bp
34,100
34,977,898
94.67
29,858
87.56
33,664
98.72
>500bp
21,519
30,504,078
94.36
18,468
85.82
21,213
98.57
>1,000bp
11,007
23,112,467
93.95
9,202
83.60
10,847
98.54
>10,000bp
28
377,698
94.11
26
92.85
28
100.0
3
Table S6 Assessment of genome coverage by ESTs of S. furcifera
With >90 % sequence
With >50 % sequence
in one scaffold
in one scaffold
Number
Number Percentage
Number Percentage
271-713bp
154
143
92.20
153
99.35
Notes: The ESTs dataset was downloaded from NCBI Genbank database
(gi74252047--gi74252202).
ESTs
Dataset
Table S7 Assessment of genome coverage by assembled transcripts of S. furcifera
With >90 % sequence in
With >50 % sequence in
Unigene
one scaffold
one scaffold
Number
Dataset
Number
Percentage
Number
Percentage
ALL
60,685
58,529
96.44
60,400
99.53
Notes: The transcripts dataset was downloaded from NCBI GEO database
(SRP009194).
4
Table S8 Genome assembly completeness evaluated based on 248 CEGs (Core Eukaryotic Genes)
S. furcifera
N. lugen
A. pisum
Type
Proteins
Completeness (%)
Proteins
Completeness (%)
Proteins
Completeness (%)
Complete
235
94.76
234
94.35
238
95.97
Group1
61
92.42
61
92.42
63
95.45
Group2
51
91.07
53
94.64
52
92.86
Group3
59
96.72
57
93.44
60
98.36
Group4
64
98.46
63
96.92
63
96.92
Partial
247
99.59
240
96.77
248
100.0
Group1
66
100.0
64
96.77
66
100.0
Group2
55
98.21
56
100
56
100.0
Group3
61
100.0
57
93.44
61
100.0
Group4
65
100.0
63
96.92
65
100.0
Notes: “Proteins” indicates number of the 248 ultra-conserved CEGs covered by genome. “% Completeness” indicates percentage of CEGs
present in genome. “Complete” indicates number of CEGs with >70 % region covered by genome. “Partial” indicates number of CEGs partially
covered by assembly.
5
Table S9 Gene numbers in each expression pattern
Category
Expression Pattern (range)
Gene Number
Pattern1
emb-1in
864
Pattern2
1in-5in
134
Pattern3
1in-10d
525
Pattern4
2in-5in
591
Pattern5
3in-4in
523
Pattern6
3in-5in
218
Pattern7
emb-5in
609
Pattern8
5d-10d
702
Total
4,166
Notes: The expression pattern here shows higher expression level than other stages.
Abbreviation: Embryo (emb), the 1st instar nymph (1in), the 2nd instar nymph (2in),
the 3rd instar nymph (3in), the 4th instar nymph (4in), the 5th instar nymph (5in), the
5-day adult (5d) and 10-day adult (10d).
6