Transcript sequencing data set
This study included 16 libraries of samples from grapes and peaches at three growth stages (Table 1). The comparison results of grape sample sequencing data are shown in Table 2. A total of 186,132,112 reads were generated, of which C_G_t2 had the largest number of reads with 29,858,769 reads. The least is C_G_t1, with 15,933,645 reads. After comparing the reads to the grape reference genome, the highest comparison rate is 77.60% (C_G_t1), the average rate of 4 samples of cultivated grapes reached 73.15%, and the average comparison rate of 4 samples of wild grapes was 59.5%. After assembly, a total of 27,264 genes and 66,713 transcripts were obtained. The length of contig N50 reached 2,715 kb, and the average length of contigs reached 1881 kb. The annotation results showed that 44,007 transcripts were completely matched to the reference genome.
Table 1
Sample abbreviation specifications
Species
|
Sample abbreviation
|
Sample description
|
Grape
|
C_G_t1
|
Fruit samples of cultivated grape 'Pinot Noir' in young fruit stage
|
C_G_t2
|
Fruit samples of cultivated grape 'Pinot Noir' in swelling stage
|
C_G_t3
|
Fruit samples of cultivated grape 'Pinot Noir' in maturity
|
C_G_leaf
|
Leaf samples of cultivated grape 'Pinot Noir' in maturity
|
W_G_t1
|
Fruit samples of wild grape 'Changbai No. 9' in young fruit stage
|
W_G_t2
|
Fruit samples of wild grape 'Changbai No. 9' in swelling stage
|
W_G_t3
|
Fruit samples of wild grape 'Changbai No. 9' in maturity
|
W_G_leaf
|
Leaf samples of wild grape 'Changbai No. 9' in maturity
|
Peach
|
C_P_t1
|
Fruit samples of cultivated peach 'Okubo' in young fruit stage
|
C_P_t2
|
Fruit samples of cultivated peach 'Okubo' in swelling stage
|
C_P_t3
|
Fruit samples of cultivated peach 'Okubo' in maturity
|
C_P_leaf
|
Leaf samples of cultivated peach 'Okubo' in maturity
|
W_P_t1
|
Fruit samples of wild peach 'Lianyungang Maotao' in young fruit stage
|
W_P_t2
|
Fruit samples of wild peach 'Lianyungang Maotao' in swelling stage
|
W_P_t3
|
Fruit samples of wild peach 'Lianyungang Maotao' in maturity
|
W_P_leaf
|
Leaf samples of wild peach 'Lianyungang Maotao' in maturity
|
Table 2
Comparison results of transcript sequencing data
Species
|
Sample abbreviation
|
Total pairs
|
Mapped reads
|
Concordant pairs
|
Grape
|
C_G_t1
|
15 933 645
|
82.80%
|
77.60%
|
C_G_t2
|
29 858 769
|
79.30%
|
73.80%
|
C_G_t3
|
22 781 342
|
76.60%
|
70.60%
|
C_G_leaf
|
25 566 026
|
75.60%
|
70.60%
|
W_G_t1
|
17 098 859
|
73.00%
|
63.40%
|
W_G_t2
|
26 403 616
|
68.90%
|
59.50%
|
W_G_t3
|
23 370 214
|
69.90%
|
60.60%
|
W_G_leaf
|
25 119 641
|
62.40%
|
54.70%
|
Peach
|
C_P_t1
|
24 512 137
|
85.20%
|
81.00%
|
C_P_t2
|
17 326 896
|
88.20%
|
84.20%
|
C_P_t3
|
30 382 911
|
88.10%
|
84.40%
|
C_P_leaf
|
16 055 962
|
87.60%
|
83.60%
|
W_P_t1
|
15 770 694
|
86.50%
|
82.20%
|
W_P_t2
|
17 409 126
|
88.20%
|
84.20%
|
W_P_t3
|
29 320 743
|
87.10%
|
84.30%
|
W_P_leaf
|
26 376 610
|
85.80%
|
81.50%
|
The comparison results of the sequencing data of the peach samples are shown in Table 2. A total of 177,155,079 reads were generated, of which C_P_t1 had the largest number of reads with 30,382,911 reads, and the smallest was W_P_t1 with 15,770,694 reads. After comparing reads to the peach reference genome, it was found that the highest comparison rate was 84.40% (C_P_t1), and the lowest was 81.00% (C_P_t3). The average comparison rate of the 4 samples of 'Okubo' reached 83.3%,' the average comparison rate of the 4 samples of 'Lianyungang Maotao' is 83.1%. A total of 27,999 genes were obtained after assembly. With 56,876 transcripts, the length of contig N50 reached 2475 kb, and the average length of contigs reached 1635 kb. The annotation results showed that 29,542 transcripts were perfectly matched to the reference genome.
Differences in transverse diameter, longitudinal diameter and single fruit weight
As the grape fruits (Fig. 1, Table 3), the horizontal and vertical diameters of cultivated grape 'Pinot Noir' have relatively large changes in the three periods. In the horizontal diameter, the expansion stage of 'Pinot Noir' increased by 2.28 mm, which was 1.25 times, compared with the young fruit stage; and the mature stage increased by 0.24 mm, which was 1.02 times, compared with the expansion stage. And it increased by 2.5 mm from the young fruit stage to the mature stage, which was 1.28 times. In the longitudinal diameter, the expansion stage of 'Pinot Noir' increased by 1.82 mm, which was 1.18 times compared with the young fruit stage; and the mature stage increased by 0.8 mm, which was 1.07 times, compared with the expansion stage, and increased by 2.6 mm, which was 1.26 times, from the young fruit stage to the mature stage.
Table 3
Sugar and acid content of cultivated and wild grapes and peach fruits in three periods
Sample
|
Soluble sugar (\(\text{m}\text{g}\bullet \text{g}\)−1)
|
Organic acid (\(\text{m}\text{g}\bullet \text{g}\)−1)
|
Sorbitol
|
Fructose
|
Glucose
|
Sucrose
|
Quinic
acid
|
Citric
acid
|
Malic
acid
|
Oxalic acid
|
Shikimic acid
|
Grape
|
C_G_t1
|
-
|
1.98
|
1.80
|
-
|
10.64
|
-
|
10.02
|
0.04
|
0.03
|
C_G_t2
|
-
|
56.00
|
51.02
|
2.50
|
1.84
|
-
|
1.27
|
0.05
|
-
|
C_G_t3
|
-
|
50.65
|
45.79
|
3.11
|
3.67
|
0.11
|
1.34
|
0.08
|
-
|
W_G_t1
|
-
|
1.04
|
0.11
|
0.05
|
11.51
|
-
|
4.87
|
0.01
|
-
|
W_G_t2
|
-
|
12.06
|
9.61
|
1.01
|
4.81
|
0.16
|
5.54
|
0.01
|
0.01
|
W_G_t3
|
-
|
21.75
|
18.99
|
2.80
|
0.60
|
0.26
|
3.54
|
0.01
|
0.01
|
Peach
|
C_P_t1
|
5.64
|
16.38
|
15.90
|
4.83
|
3.01
|
0.01
|
3.58
|
0.22
|
-
|
C_P_t2
|
6.27
|
7.38
|
7.01
|
20.30
|
0.77
|
0.35
|
1.24
|
0.10
|
0.02
|
C_P_t3
|
0.86
|
9.63
|
9.56
|
28.15
|
1.23
|
-
|
2.95
|
0.31
|
0.04
|
W_P_t1
|
5.21
|
3.54
|
24.03
|
6.98
|
6.49
|
-
|
8.70
|
0.73
|
0.26
|
W_P_t2
|
3.00
|
2.45
|
4.67
|
4.87
|
3.19
|
2.28
|
4.38
|
0.57
|
0.13
|
W_P_t3
|
0.92
|
0.95
|
3.78
|
9.45
|
0.30
|
-
|
0.56
|
0.13
|
0.01
|
The horizontal and vertical diameters of the wild grape 'Changbai No. 9' have relatively small changes in the three periods. For the horizontal diameter, the expansion stage and young fruit stage of 'Changbai No. 9' are basically the same, and the mature stage is 0.61 mm longer than the expansion stage, which was 1.02 times. From the young fruit stage to the mature stage, the increase was 0.54 mm, which was 1.06 times. For the longitudinal diameter, the swelling stage and the young fruit stage of 'Changbai No. 9' are basically the same. The mature stage is 0.85 mm, which was 1.09 times longer than the swelling stage, and 0.68 mm, which was 1.07 times from the young fruit stage to the mature stage.
The cultivated and wild grapes maintain the same changing trend in fruit weight per fruit. During the three periods, the weight gradually increased with the growth and development of the fruit. The change of fruit weight of the cultivated grape 'Pinot Noir' in the three periods is more significant than that of the wild grape 'Changbai No. 9' (Fig. 2). The single fruit weight of 'Pinot Noir' increased by 0.41 g at swelling period, which was 1.75 times compared with the young fruit period; and the mature period increased by 0.05 g, which was 1.06 and 1.85 times when compared with the swelling period and the young fruit stage respectively. The single fruit weight of the wild grape 'Changbai No. 9' has a small change compared with the cultivated grape 'Pinot Noir'. The single fruit weight of 'Changbai No. 9' was basically the same in the swelling stage and the young fruit stage, and the ripening stage was increased by 0.1 g compared with the swelling stage, which was 1.18 times. And the mature stage was 0.12 g more than the young fruit stage, which was 1.22 times. The growth rate of the cultivated grape 'Pinot Noir' increased significantly compared with the wild grape 'Changbai No. 9', especially from the young fruit stage to the expansion stage, while the growth rate of the 'Changbai No. 9' was more obvious from the expansion stage to the mature stage.
The horizontal and vertical diameters of cultivated peach 'Okubo' vary greatly in the three periods (Fig. 1, Table 3). For the horizontal diameter, the expansion period of wild peach 'Okubo' increased by 33.15 mm compared with the young fruit stage, which was 2.28 times. Compared with the swelling stage, the mature period increased by 18.18 mm, which was 1.31 times. And the total increase from the young fruit stage to the mature stage was 51.3 mm, which was 2.98 times of the young fruit stage. For the longitudinal diameter, the swelling stage of cultivated peach 'Okubo' increased by 24.46 mm, which was 1.77 times, compared with the young fruit stage, while the mature stage increased by 10.15 mm, which was 1.18 times, compared with the swollen stage. And the total increase from the young fruit stage to the mature stage increased by 34.61 mm, which was 2.09 times.
In terms of the single fruit weight of peach fruit, the fruit weight of cultivated peach 'Okubo' changed significantly in the three stages. The expansion stage increased by 96.85 g, which was 9.79 times, compared with the young fruit stage, and the mature stage increased by 126.97 g, which was 2.18 times, compared with the expansion stage. Compared with the young fruit stage, the mature stage increased by 223.82 g, which was 21.32 times.
The horizontal and vertical diameter changes of the wild peach 'Lianyungang Maotao' in the three stages are smaller than that of the 'Okubo'. For the horizontal diameter, the expansion period of the wild peach 'Lianyungang Maotao' increased by 5.8 mm compared with the young fruit stage, which was 2.28 times at the mature stage. Compared with the swelling period, it increased by 17.21 mm, which was 1.31 times. From the young fruit stage to the mature stage, total increase was 23.01 mm, which was 2.99 times. For the longitudinal diameter, the swelling stage of the wild peach 'Lianyungang Maotao' increased by 4.24 mm, which was 1.77 times compared with the young fruit stage, and the mature stage increased by 11.62 mm, which was 1.18 times compared with the swollen stage, and the total increase from the young fruit stage to the mature stage increased by 15.85 mm, which was 2.09 times.
The individual fruit weight of the wild peach 'Lianyungang Peach' has relatively little change. The mature stage increases by 34.91 g, which was 4.27 times compared with the expansion stage, and the total increase by 40.6 g, which was 9.12 times compared with the young fruit stage.
Combining the above results, it can be seen that the cultivated peach 'Okubo' has a higher growth rate than the wild peach 'Lianyungang Maotao', and it is dominant in the transverse diameter, longitudinal diameter and single fruit weight, and the skin color of fruit is more red.
Difference in soluble sugar and organic acid content of fruit
Soluble sugars in grape and peach fruits include sorbitol, fructose, glucose, and sucrose, and organic acids include quinic acid, citric acid, malic acid, oxalic acid, and shikimic acid. As shown in Table 3, the total sugar content of cultivated grape 'Pinot Noir' increased from 3.78 mg·g− 1 to 99.55 mg·g− 1, with an increase of 95.77 mg·g− 1 from the first stage to the third stage, while the sugar content of 'Changbai No.9' increased from 1.2 mg·g− 1 to 43.54 mg·g− 1, with increase of 42.34 mg·g− 1. In terms of sugar content, the increase of 'Pinot Noir' is 53.43 mg·g− 1 more than that of 'Changbai No.9', which was 2.26 times.
The average sugar-acid ratio of 'Pinot Noir' is 4.27 times that of 'Changbai No.9', which was 18.13. The average sugar-acid ratio of 'Changbai No.9' is 4.25. At maturity stage, the sugar-to-acid ratio of 'Pinot Noir' is 1.86 times that of 'Changbai No. 9', reached 19.56, and that of 'Changbai No. 9' is 10.49. It can be seen that the sugar content of the cultivated grape 'Pinot Noir' in the three periods is higher than that of the wild grape 'Changbai No.9'. And the sugar-acid ratio is higher, means an advantage in fruit sweetness. For the cultivated grape 'Pinot Noir', the content of fructose and glucose changed significantly. From the young fruit stage to the mature stage, the fructose content increased by 48.67 mg·g− 1 and the glucose content increased by 43.99 mg·g− 1. From the expansion stage to the mature stage, the sucrose increased to 3.11 mg·g− 1. Compared with the cultivated grape 'Pinot Noir', the wild grape 'Changbai No.9' has a small increase in soluble sugar content. From the young fruit stage to the swelling stage, the fructose content increased by 11.02 mg·g− 1, the glucose increased by 9.5mg·g− 1, and the sucrose only increased by 0.96 mg·g− 1. From the expansion stage to the mature stage, the fructose content increased by 9.69 mg·g− 1, glucose increased by 9.38 mg·g− 1, and sucrose increased by 2.8 mg·g− 1. The content of quinic acid in the cultivated grape 'Pinot Noir' decreased from 6.97 mg·g− 1 to 3.67 mg·g− 1 from the young fruit stage to the mature stage, and the wild cultivar 'Changbai No.9' decreased by 10.91 mg·g− 1 to 0.6 mg·g− 1in the same period. The content of malic acid in 'Pinot Noir' decreased from 8.68 mg·g− 1 from the young fruit stage to the mature stage to 1.34 mg·g− 1. And in the same period, the content of 'Changbai No.9' decreased from 1.33 mg·g− 1 to 3.54 mg·g− 1. The content of oxalic acid in 'Pinot Noir' ranges from 0.04 mg·g− 1 in the young fruit stage to 0.08 mg·g− 1 in the mature stage, while the content of 'Changbai No.9' has been maintained at 0.01 mg·g− 1. In terms of citric acid content, 'Pinot Noir' maintains a low level, with a content of 0.11 mg·g− 1 in the mature stage, and a citric acid content of 0.26 mg·g− 1 in 'Changbai No.9'.
The soluble sugar content of cultivated peach 'Okubo' is higher than that of wild peach 'Lianyungang Maotao' at every stage, and the organic acid content was lower. The total soluble sugar content of cultivated peach 'Okubo' increased from 42.75 mg·g− 1 to 48.2 mg·g− 1, while the total soluble sugar content of wild peach 'Lianyungang Maotao' decreased from 39.76 mg·g− 1 to 15.1 mg·g− 1. In terms of total soluble sugar content, cultivated peach 'Okubo' increased 30.11 mg·g− 1 more than wild peach 'Lianyungang Maotao'. The total organic acid content of the cultivated peach 'Okubo' increased from 6.82 mg·g− 1 to 4.53 mg·g− 1, which increased 2.29 mg·g− 1, while the total organic acid content of the wild peach 'Lianyungang Maotao' decreased from 16.18 mg·g− 1 to 1 mg·g− 1. In terms of total organic acid content, the reduction of wild peach 'Lianyungang Maotao' is 12.89 mg·g− 1 more than that of cultivated peach 'Okubo'. The sucrose content of cultivated peach 'Okubo' and wild peach 'Lianyungang Maotao' maintained an increasing trend during the three periods. The sucrose content of cultivated peach 'Okubo' ranged from 4.83 mg·g− 1 to 28.18 mg·g− 1, accounting for 58% of the total soluble sugar content. The sucrose content of wild peach 'Lianyungang Maotao' ranges from 6.98 mg·g− 1 to 9.45 mg·g− 1, accounting for 62% of the total soluble sugar content, and the content of all other soluble sugars showed a downward trend. The content of quinic acid and malic acid in the cultivated peach 'Okubo' and the wild peach 'Lianyungang Maotao' decreased significantly in the three periods.
Analysis of gene differential expression in cultivated and wild grapes and peach
The volcano diagram of the relative changes in expression level of grapes in each period (Fig. 3A), which is comparing the transcripts of 'Changbai No. 9' to the transcripts of 'Pinot Noir'. The results showed that in the young fruit stage, the number of up-regulated transcripts was 1,552 and the number of down-regulated transcripts was 737; in the swelling stage, the number of up-regulated transcripts was 747, and the number of down-regulated transcripts was 1,284. In the mature stage, the number of up-regulated transcripts was 733, and the number of down-regulated transcripts was 1,036. It can be seen that the transcripts of 'Pinot Noir' are more active in the young fruit stage, and more transcripts are up-regulated. In the expansion and maturity stages, number of upward adjustments is more. A total of 55,956 transcripts were expressed in 'Pinot Noir', and a total of 53,446 transcripts were expressed in 'Changbai No. 9', with 49,232 co-expressed transcripts. After the differential expression screening of the transcript expression level, it was found that the differential transcripts in the young fruit stage, the swelling stage, and the mature stage gradually decreased. There were 3,505, 3,077 and 2,707 differential transcripts respectively (Fig. 4A), and a total of 878 common transcripts in the three periods. There are 6,086 common differential transcripts and a total of 6,086 non-repetitive differential transcripts.
The differential expression analysis of peach transcripts was performed (Fig. 3B). Compared with 'Lianyungang Maotao', 'Okubo' contains 636, 989, 1890 up-regulated transcripts at three stages respectively, and 1082, 915, 2716 down-regulated transcripts respectively. In the young fruit stage and the mature stage, the transcripts of 'Okubo' are more active, and there are more transcripts up-regulated. In 'Okubo', a total of 46,172 transcripts were expressed, and in 'Lianyungang Maotao', a total of 46,372 transcripts were expressed. According to the selection criteria of P-value < 0.05 and ཛྷFold Changeཛྷ> 1, significantly differentially expressed transcripts were screened (Fig. 4B). The results showed that the number of differentially expressed transcripts in the young fruit stage and the swelling stage were similar, 907 and 957 respectively. The number of differentially expressed transcripts in the mature stage was larger, which was 3540. There are 301 common differentially expressed transcripts in the young fruit stage, swelling stage and mature stage.
STEM analysis of differentially expressed genes
Time series analysis of 878 and 301 co-differentially expressed genes in grape and peach was performed by STEM software. As shown in Fig. 5, the differentially expressed genes of 'Pinot Noir' are divided into 16 modules, of which there are 5 modules with significant differential expression, namely modules 0, 4, 11, 14, and 15, of which module 4 contains the most genes, reached 259, and module15 is the least, with only 42. There are 3 significant modules in 'Changbai No. 9', namely moudle 3, 4 and 14, of which module4 has the most genes (113). Module3 has 34 genes. The expression trends of the two grape species in the module are same, and the difference is mainly reflected in the expression level of the genes. In the two different significant expression modules 0, 3, 11, and 15, the expression level of 'Pinot Noir' is higher than that of 'Changbai No. 9'. In the same significant expression module14, it was first up-regulated and then down-regulated, and the expression level of 'Changbai No. 9' in this module was higher.
It can be seen from Fig. 5 that the genes of 'Okubo' are significantly clustered in 4 modules (12, 13, 14, 15), and the genes of 'Lianyungang Maotao' are significantly clustered in 5 modules (11, 12, 13, 14, 15). Module14 and Module15 in 'Okubo' are the most representative modules. The expected distribution genes are 14.6 and 13.3, respectively, and the actual distribution genes are 49.5 and 45. The most representative modules in 'Lianyungang Maotao' are module11 and module14, the expected distribution genes are 19.8 and 15.4, respectively, and the actual distribution genes are 33 and 56.5. Similar expression patterns are maintained in the common modules (12, 13, 14, 15) of 'Okubo' and 'Lianyungang Maotao'. The difference between the two modules is mainly reflected in the amount of expression. In module12, the average expression level of 'Lianyungang Maotao' is higher, reached 167.4, and that of 'Okubo' is 113.9. On module13, the expression of 'Okubo' was more active, reached 52.5, and the expression of 'Lianyungang Maotao' was 33.8. On the module14, the expression levels of 'Okubo' and 'Lianyungang Maotao' were significantly different, which was 68.9 and 37.9, respectively. On the module 15, the expression levels of 'Okubo' were lower than that of the 'Lianyungang Maotao', which was 26.6 and 42.8 respectively. The significant expression module No. 11 of 'Lianyungang Maotao' is not significant in 'Okubo'. Therefore, after analyzing the function of the transcript in this module, it is found that its function is mainly concentrated in the overall composition of the membrane, chloroplast, and chloroplast thylakoid membrane, iron ion binding, chlorophyll binding, flavonoid biosynthesis process, anti-stress response and photosynthesis, etc.
Analysis of co-expression network of differential expressed genes
The 878 and 301 common differential expressed genes of grapes and peaches were analyzed by weighted gene co-expression network analysis (WGCNA), and their subsequent co-expression modules were studied to reveal their differences. According to the expression level of the transcript, a cluster dendrogram was made for the grapes in the three periods. The expression level of 'Changbai No. 9' in the young fruit stage is quite different from that of other samples (Fig. 6A), while the samples in the expansion stage and mature period appeared clustered. Six modules are finally obtained with the 878 genes of grapes, of which module Turquoise, Blue, Brown, Yellow and Green contains 302, 241, 156, 104 and 70 genes respectively (Fig. 6C). Grey module including genes not belonging to any modules with no function.
The function of the genes in the Turquoise module is mainly related to the overall composition of the membrane and the response to low temperature stress. The genes in the Blue module are related to the nucleus and plasma membrane. The genes in the Brown module are related to the heat stress response and cytoplasm. The genes in the Yellow module are related to the binding of metal ions and the transcript DNA template. And the Green module is related to the overall composition of the nucleus and membrane.
Analysis of the 301 common differential genes of 'Okubo' and 'Lianyungang Maotao' found that the expression level of 'Lianyungang Maotao' at the maturity stage (W_P_t3) was significantly different from other samples (Fig. 6B). As shown in Fig. 6D, 4 modules are finally formed, of which Turquoise module contains 183 genes, Blue module contains 56 genes, Brown module contains 35 genes, and grey module with no function. After annotating the genes function in each module, it is found that the genes in the Turquoise module are mainly enriched in the cytoplasm, ATP binding and stress resistance; the genes in the Blue module are mainly concentrated in the nucleus, DNA binding and stress resistance; the genes in the Brown module are mainly enriched in the overall composition of the membrane, chlorophyll binding and photosynthesis.
Differentially expressed genes GO function enrichment analysis
878 and 301 co-expressed genes of grape and peach were analyzed by GO enrichment. The 878 common differentially expressed genes of 'Pinot Noir' and 'Changbai No. 9' have 6 annotations at the Cellular component, 12 annotations at the Molecule function, and 16 annotations at the Biological process (Table 4). In terms of cell components, annotations are mainly focused on integral component of membrane, nucleus, plasma membrane, mitochondrion, golgi membrane and nucleoplasm. In terms of molecular functions, annotations mainly focus on ATP binding, zinc ion binding, DNA binding, sequence-specific DNA binding transcription factor activity, RNA binding, and protein serine/threonine kinase activity. In the biological process, annotations mainly focus on transcription, DNA-templated, regulation of transcription, DNA-templated, defense response, protein transport, embryo development ending in seed dormancy and mRNA processing.
Table 4
GO function enrichment analysis of common differential expression genes of cultivated and wild grape species
GO
|
GO term
|
Number
|
P-value
|
Cellular Component
|
integral component of membrane
|
119
|
2.19E-04
|
nucleus
|
96
|
3.44E-09
|
plasma membrane
|
79
|
2.32E-02
|
mitochondrion
|
27
|
5.91E-03
|
Golgi membrane
|
9
|
2.77E-02
|
nucleoplasm
|
2
|
1.59E-02
|
Molecular Function
|
ATP binding
|
58
|
3.11E-26
|
zinc ion binding
|
36
|
1.63E-02
|
DNA binding
|
30
|
1.14E-08
|
sequence-specific DNA binding transcription factor activity
|
20
|
2.09E-06
|
RNA binding
|
19
|
8.57E-03
|
protein serine/threonine kinase activity
|
11
|
9.39E-15
|
ligase activity
|
9
|
1.83E-02
|
nucleic acid binding
|
3
|
4.76E-03
|
phosphoprotein phosphatase activity
|
2
|
4.90E-02
|
calmodulin binding
|
2
|
4.38E-03
|
serine-type endopeptidase activity
|
1
|
2.13E-02
|
ADP binding
|
1
|
3.36E-23
|
Biological Process
|
transcription, DNA-templated
|
38
|
2.00E-08
|
regulation of transcription, DNA-templated
|
25
|
1.41E-06
|
defense response
|
17
|
2.54E-10
|
protein transport
|
8
|
4.18E-02
|
embryo development ending in seed dormancy
|
6
|
2.04E-02
|
mRNA processing
|
4
|
2.47E-03
|
plant-type hypersensitive response
|
3
|
2.26E-04
|
metabolic process
|
2
|
3.80E-02
|
flower development
|
2
|
4.05E-03
|
DNA replication
|
1
|
1.08E-02
|
DNA repair
|
1
|
8.21E-05
|
DNA recombination
|
1
|
2.13E-02
|
intracellular protein transport
|
1
|
1.96E-02
|
mitotic nuclear division
|
1
|
1.81E-02
|
chromatin modification
|
1
|
1.87E-02
|
The GO function enrichment analysis of 301 common differentially expressed genes of peaches found that there are 10 annotations at the Cellular component, 8 annotations at the Molecule function, and 4 annotations at the Biological process(Table 5). In terms of cell components, annotations are focused on integral component of membrane, nucleus、chloroplast, plasma membrane, cytosol, mitochondrion, endoplasmic reticulum membrane, golgi apparatus, nucleolus and chloroplast stroma. In terms of molecular functions, annotations are concentrated on ATP binding, metal ion binding, DNA binding, protein serine/threonine kinase activity, zinc ion binding, RNA binding, sequence-specific DNA binding transcription factor activity and GTP binding. In terms of biological processes, annotations focus on regulation of transcription, DNA-templated, transcription, DNA-templated, mRNA processing and protein ubiquitination.
Table 5
GO function enrichment analysis of 301 common differential expression genes of cultivated and wild peach species
GO
|
GO term
|
Number
|
P-value
|
Cellular Component
|
integral component of membrane
|
28
|
7.89E-06
|
nucleus
|
21
|
6.28E-09
|
chloroplast
|
14
|
4.63E-02
|
plasma membrane
|
10
|
7.02E-07
|
cytosol
|
7
|
1.14E-03
|
mitochondrion
|
5
|
1.09E-03
|
endoplasmic reticulum membrane
|
3
|
4.55E-02
|
Golgi apparatus
|
3
|
1.80E-02
|
nucleolus
|
2
|
2.94E-02
|
chloroplast stroma
|
1
|
1.00E-02
|
Molecular Function
|
ATP binding
|
26
|
1.64E-05
|
metal ion binding
|
11
|
1.05E-03
|
DNA binding
|
9
|
6.90E-05
|
protein serine/threonine kinase activity
|
6
|
4.32E-04
|
zinc ion binding
|
5
|
1.86E-04
|
RNA binding
|
4
|
4.88E-03
|
sequence-specific DNA binding transcription factor activity
|
2
|
6.51E-06
|
GTP binding
|
1
|
4.67E-02
|
Biological Process
|
regulation of transcription, DNA-templated
|
8
|
2.99E-03
|
transcription, DNA-templated
|
7
|
7.85E-07
|
mRNA processing
|
1
|
3.08E-02
|
protein ubiquitination
|
1
|
4.45E-03
|
The differentially expressed genes of cultivated and wild materials in our study have similar items in GO functional enrichment analysis. Cell component included integral component of membrane, nucleus, plasma membrane, and mitochondrion; molecular functions included ATP binding and zinc ion binding, DNA binding, sequence-specific DNA binding transcription factor activity, RNA binding, and protein serine/threonine kinase activity; biological processes included regulation of transcription, DNA-templated, transcription, DNA-templated, and mRNA processing.
Differentially expressed genes KEGG pathway enrichment analysis
KEGG pathway enrichment analysis was performed on 878 and 301 common differentially expressed genes of cultivated and wild materials to explore the function of genes in the plant growth process from multiple angles. The 878 common differentially expressed genes of 'Pinot Noir' and 'Changbai No. 9' gathered in 103 pathways. The functions are mainly concentrated in metabolic pathways, biosynthesis of secondary metabolites, protein processing in the endoplasmic reticulum, carbon metabolism, glutathione metabolism, amino acid biosynthesis, phenylpropane biosynthesis, peroxisomes, glycolysis/glycolysis raw and pyruvate metabolism etc. According to the results of KEGG and GO analysis, a total of ten genes related to grape resistance, fruit color, peel color and fruit flavor were screened. Among them, there are five genes related to grape fruit resistance: superoxide dismutase (SOD2), glutathione S-transferase (GST), serine/threonine-protein kinase (PBS1), basic endochitinase B (CHIB) and calreticulin (CALR); fruit size is related two genes: auxin-responsive protein (IAA) and ABA responsive element binding factor (ABF); two fruit flavor-related genes: malate dehydrogenase (MDH1) and pyruvate kinase (PK); one peel color-related gene: chalcone synthase (CHS).
The 301 common genes of 'Okubo' and 'Lianyungang Maotao' clustered in 51 pathways. The functions of the differential genes are mainly concentrated in metabolic pathways, flavonoid biosynthesis, tyrosine metabolism, pyrimidine metabolism, alpha-linolenic acid metabolism, photosynthesis, pyruvate metabolism, photosynthesis-antenna proteins, pantothenate and CoA biosynthesis. These pathways may be closely related to the differences in the traits of 'Okubo' and 'Lianyungang Maotao' in peel color, fruit weight, sugar and acid content. Combining the results of KEGG pathway enrichment analysis and GO function annotation results, it was found that 12 genes were related to peach fruit resistance, peel color and fruit growth. Among them, eight genes are related to fruit resistance: polyphenol oxidase, peroxidase, glutathione S-transferase (GST), chitinase, 12-oxophytodienoic acid reductase (OPR), light-harvesting complex II chlorophyll a/b binding protein 4 (LHCB4), 9-cis-epoxycarotenoid dioxygenase (NCED) and alcohol dehydrogenase class-P (ADH1); there are three genes related to fruit color: chalcone synthase (CHS), phenylalanine ammonia-lyase (PAL) and bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR). And one gene related to fruit growth: SAUR family protein (SAUR). Considering KEGG annotations in grapes and peaches: metabolic pathways and pyruvate metabolism are the common pathways, which may explain the differences between cultivated and wild fruit trees.