Table S1. Primers for validated gene expression in adventitious root formation
Genes
Sense-primer
Antisense-primer
Cycles
Protein
binding/ubiquitin-protein
ligase 1
RAR1
Chalcone synthase
Aquaporin
Non-symbiotic
hemoglobin protein
PPO1
Phosphoserine
aminotransferase
Heat shock protein
alcohol dehydrogenases
Maact
CCACATCACTTTTCACGA
CTTTGCTCCATTGCTCTC
40
TTTCCACCCTCTCATTCG
CGAGGAAGGTGTCGTTGG
CGAGGAAGGTGTCGTTGG
CAACAGGGAAATAGCACC
TCCCCACTCCCACAACAA
GTAGCCATCGGCGAGAGA
GTAGCCATCGGCGAGAGA
TCAGGGTAATGAGGAGCC
40
40
40
40
GCGTCAAGTTCCCAATAA
ATGGAGATGAGCCACAGA
ACTTCCTCTTCGTCCTCC
ACGGCGTAGTCATCGGGG
40
40
GGCTCATTGATAATACGC
GCGGATGACGCAACGGAT
GTTCCTGCTCGTAGTCCAA
CTGTCCCTGCCTACTTCA
ATTCATCACTCACTCGGT
CCATGCTATTCTCCGTCTC
40
40
40
Table S2. Overview of sequencing and assembly.
Sequences
S0
S1
S2
Number of raw reads
Average lengths (bp)
The total length (G)
Number of fail reads
Trimmed reads
Number of reads after trimming
Percentage trimmed
Avg. length after trimming (bp)
74,975,982
101
7.66
2148
17,998,658
74,973,834
24.0%
90.7bp
74,977,304
101
7.66
2702
17,999,742
74,974,602
24.0%
90.7 bp
87,424,447
101
8.89
598
16,964,392
87,423,809
24.0%
90.2 bp
Table S3. Contig analysis statistics
Contig
S0
S1
S2
Number of contigs
69,058
69,087
66,557
Length of all contigs (nt)
49.9 M
49.9 M
50.1 M
Average contig size (bp)
722
722
753
Range of contig length (bp)
134-11304
114-11,303
122-20,054
Table S4. Uniprot annotation analysis statistics
Sequences
S0
S1
S2
Uniprot annotaion
39,504
39,497
31,868
Unknow contig
29,554
29,590
34,689
Annotation rate (%)
57.20
57.17
47.88
Table S5. The main GO terms in the libraries of S0 S1 and S2 stages
GO_term
Main five cellular component terms
cell
cell part
organelle
macromolecular complex
organelle part
Main five molecular function terms
binding
catalytic activity
transporter activity
structural molecule activity
nucleic acid binding transcription factor activity
Main five biological process terms
metabolic process
cellular process
biological regulation
regulation of biological process
localization
GO_id
gene_number in S0 gene_number in S1 gene_number in S2
GO:0005623
GO:0044464
GO:0043226
GO:0032991
GO:0044422
9,861
9,861
4,160
2,163
1,260
9,853
9,853
4,160
2,153
1,252
7,693
7,693
3,456
1,439
871
GO:0005488
GO:0003824
GO:0005215
GO:0005198
GO:0001071
15,926
14,014
1,633
878
627
15,931
13,980
1,623
877
627
13,900
11,183
1,173
534
521
GO:0008152
GO:0009987
GO:0065007
GO:0050789
GO:0051179
16,028
14,027
2,699
2,658
2,639
16,007
14,006
2,699
2,658
2,623
13,032
12,144
2,155
2,132
1,913
Table S6. Unique pathways in S1 and S2 stages
PATHWAY_I
D
PATHWAY_DES
Unique pathway in the S1 stage
ko02030
Bacterial chemotaxis
Biosynthesis of siderophore group nonribosomal
ko01053
peptides
ko00905
Brassinosteroid biosynthesis
ko00473
D-Alanine metabolism
ko00472
D-Arginine and D-ornithine metabolism
ko00351
DDT degradation
ko00621
Dioxin degradation
ko04512
ECM-receptor interaction
ko00642
Ethylbenzene degradation
ko02040
Flagellar assembly
ko04640
Hematopoietic cell lineage
ko00550
Peptidoglycan biosynthesis
ko02060
Phosphotransferase system (PTS)
ko00622
Xylene degradation
Unique pathway in the S2 stage
ko01051
Biosynthesis of ansamycins
ko04975
Fat digestion and absorption
ALL_KO_numbe
r in the pathway
Contig_
Singlet_NUM
26
16
32
1
8
5
2
7
13
56
7
37
78
37
75
20
5
7
1
2
1
1
5
4
1
7
6
1
2
0
2
2
ko00532
Glycosaminoglycan biosynthesis - chondroitin
sulfate
21
1
Figure S1. Morphological changes during Adventitious roots formation. Each stage from the beginning to the end
was referring to initial formation of callus, initial formation of callus, induction of Adventitious roots, root-like
protuberances formation and elongation of Adventitious roots.
Figure S2. Contig size distribution.
Figure S3. Changes in gene expression in samples at different stages. Numbers of up-regulated and down-regulated
genes are summarized.
Figure S4. GO categories of the DEGs in the S1 vs S2 stages
Figure S5. Confirmation of the expression profiles of selected genes by qRT-PCR