Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (6): 198-210.doi: 10.13560/j.cnki.biotech.bull.1985.2021-1151
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XIN Jian-pan(), LI Yan, ZHAO Chu, TIAN Ru-nan()
Received:
2021-09-07
Online:
2022-06-26
Published:
2022-07-11
Contact:
TIAN Ru-nan
E-mail:jianpanxin@njfu.edu.cn;tianrunan@njfu.edu.cn
XIN Jian-pan, LI Yan, ZHAO Chu, TIAN Ru-nan. Transcriptome Sequencing in the Leaves of Pontederia cordata with Cadmium Exposure and Gene Mining in Phenypropanoid Pathways[J]. Biotechnology Bulletin, 2022, 38(6): 198-210.
Min length/bp | Max length/bp | Mean length/bp | N50 | N90 | |
---|---|---|---|---|---|
Transcripts | 201 | 25 638 | 1 542 | 2 554 | 746 |
Unigenes | 201 | 25 638 | 1 753 | 2 609 | 883 |
Table 1 Length distribution of assembled transcripts and unigenes
Min length/bp | Max length/bp | Mean length/bp | N50 | N90 | |
---|---|---|---|---|---|
Transcripts | 201 | 25 638 | 1 542 | 2 554 | 746 |
Unigenes | 201 | 25 638 | 1 753 | 2 609 | 883 |
数据库 Annotated database | Unigenes数量 Number of unigenes | 占比 Percentage/% |
---|---|---|
Annotated in NR | 158 229 | 71.47 |
Annotated in NT | 107 290 | 48.46 |
Annotated in KO | 67 629 | 30.54 |
Annotated in SwissProt | 121 487 | 54.87 |
Annotated in PFAM | 98 391 | 44.44 |
Annotated in GO | 98 391 | 44.44 |
Annotated in KOG | 49 597 | 22.40 |
Annotated in all databases | 22 729 | 10.26 |
Annotated in at least one database | 170 175 | 76.86 |
Total unigenes | 221 392 | 100 |
Table 2 Unigene annotation of P. cordatas leaves
数据库 Annotated database | Unigenes数量 Number of unigenes | 占比 Percentage/% |
---|---|---|
Annotated in NR | 158 229 | 71.47 |
Annotated in NT | 107 290 | 48.46 |
Annotated in KO | 67 629 | 30.54 |
Annotated in SwissProt | 121 487 | 54.87 |
Annotated in PFAM | 98 391 | 44.44 |
Annotated in GO | 98 391 | 44.44 |
Annotated in KOG | 49 597 | 22.40 |
Annotated in all databases | 22 729 | 10.26 |
Annotated in at least one database | 170 175 | 76.86 |
Total unigenes | 221 392 | 100 |
序号 No. | 通路 Pathway | 通路_ID Pathway_ID | Unigenes数量 Numbers of unigenes |
---|---|---|---|
1 | 苯丙素生物合成Phenylpropanoid biosynthesis | ko00940 | 696 |
2 | 缬氨酸、亮氨酸和异亮氨酸降解Valine,leucine and isoleucine degradation | ko00280 | 621 |
3 | 萜类化合物骨架生物合成Terpenoid backbone biosynthesis | ko00900 | 597 |
4 | 类胡萝卜素生物合成Carotenoid biosynthesis | ko00906 | 488 |
5 | 酪氨酸代谢Tyrosine metabolism | ko00350 | 426 |
6 | 泛醌及其他萜类醌生物合成Ubiquinone and other terpenoid-quinone biosynthesis | ko00130 | 370 |
7 | 苯丙氨酸、酪氨酸和色氨酸生物合成Phenylalanine,tyrosine and tryptophan biosynthesis | ko00400 | 346 |
8 | 烟酸和烟酰胺代谢Nicotinate and nicotinamide metabolism | ko00760 | 326 |
9 | 苯丙烷代谢Phenylalanine metabolism | ko00360 | 291 |
10 | 色氨酸代谢Tryptophan metabolism | ko00380 | 269 |
11 | 类固醇生物合成Steroid biosynthesis | ko00100 | 235 |
12 | 类黄酮生物合成Flavonoid biosynthesis | ko00941 | 222 |
13 | 异喹啉生物碱生物合成Isoquinoline alkaloid biosynthesis | ko00950 | 216 |
14 | 莨菪烷、哌啶和吡啶生物碱生物合成Tropane,piperidine and pyridine alkaloid biosynthesis | ko00960 | 197 |
15 | 玉米素生物合成Zeatin biosynthesis | ko00908 | 197 |
16 | 二苯乙烯、二芳基庚烷和姜酚生物合成Stilbenoid,diarylheptanoid and gingerol biosynthesis | ko00945 | 155 |
17 | 亮氨酸代谢Linoleic acid metabolism | ko00591 | 143 |
18 | 缬氨酸、亮氨酸和异亮氨酸生物合成Valine,leucine and isoleucine biosynthesis | ko00290 | 139 |
19 | 柠檬烯和蒎烯降解Limonene and pinene degradation | ko00903 | 128 |
20 | 油菜素内酯生物合成Brassinosteroid biosynthesis | ko00905 | 97 |
21 | 二萜生物合成Diterpenoid biosynthesis | ko00904 | 83 |
22 | 黄酮和黄酮醇生物合成Flavone and flavonol biosynthesis | ko00944 | 55 |
23 | 芥子油苷生物合成Glucosinolate biosynthesis | ko00966 | 58 |
24 | 单萜的生物合成Monoterpenoid biosynthesis | ko00902 | 48 |
25 | 倍半萜和三萜生物合成Sesquiterpenoid and triterpenoid biosynthesis | ko00909 | 44 |
26 | 咖啡因代谢Caffeine metabolism | ko00232 | 28 |
27 | 花青素生物合成Anthocyanin biosynthesis | ko00942 | 14 |
29 | 甜菜红碱生物合成Betalain biosynthesis | ko00965 | 10 |
30 | 异黄酮生物合成Isoflavonoid biosynthesis | ko00943 | 6 |
31 | 吲哚生物碱生物合成Indole alkaloid biosynthesis | ko00901 | 1 |
Table 3 Unigenes for KEGG pathway annotation involved in the secondary metabolites in the leaves of P. cordata with cad-mium exposure
序号 No. | 通路 Pathway | 通路_ID Pathway_ID | Unigenes数量 Numbers of unigenes |
---|---|---|---|
1 | 苯丙素生物合成Phenylpropanoid biosynthesis | ko00940 | 696 |
2 | 缬氨酸、亮氨酸和异亮氨酸降解Valine,leucine and isoleucine degradation | ko00280 | 621 |
3 | 萜类化合物骨架生物合成Terpenoid backbone biosynthesis | ko00900 | 597 |
4 | 类胡萝卜素生物合成Carotenoid biosynthesis | ko00906 | 488 |
5 | 酪氨酸代谢Tyrosine metabolism | ko00350 | 426 |
6 | 泛醌及其他萜类醌生物合成Ubiquinone and other terpenoid-quinone biosynthesis | ko00130 | 370 |
7 | 苯丙氨酸、酪氨酸和色氨酸生物合成Phenylalanine,tyrosine and tryptophan biosynthesis | ko00400 | 346 |
8 | 烟酸和烟酰胺代谢Nicotinate and nicotinamide metabolism | ko00760 | 326 |
9 | 苯丙烷代谢Phenylalanine metabolism | ko00360 | 291 |
10 | 色氨酸代谢Tryptophan metabolism | ko00380 | 269 |
11 | 类固醇生物合成Steroid biosynthesis | ko00100 | 235 |
12 | 类黄酮生物合成Flavonoid biosynthesis | ko00941 | 222 |
13 | 异喹啉生物碱生物合成Isoquinoline alkaloid biosynthesis | ko00950 | 216 |
14 | 莨菪烷、哌啶和吡啶生物碱生物合成Tropane,piperidine and pyridine alkaloid biosynthesis | ko00960 | 197 |
15 | 玉米素生物合成Zeatin biosynthesis | ko00908 | 197 |
16 | 二苯乙烯、二芳基庚烷和姜酚生物合成Stilbenoid,diarylheptanoid and gingerol biosynthesis | ko00945 | 155 |
17 | 亮氨酸代谢Linoleic acid metabolism | ko00591 | 143 |
18 | 缬氨酸、亮氨酸和异亮氨酸生物合成Valine,leucine and isoleucine biosynthesis | ko00290 | 139 |
19 | 柠檬烯和蒎烯降解Limonene and pinene degradation | ko00903 | 128 |
20 | 油菜素内酯生物合成Brassinosteroid biosynthesis | ko00905 | 97 |
21 | 二萜生物合成Diterpenoid biosynthesis | ko00904 | 83 |
22 | 黄酮和黄酮醇生物合成Flavone and flavonol biosynthesis | ko00944 | 55 |
23 | 芥子油苷生物合成Glucosinolate biosynthesis | ko00966 | 58 |
24 | 单萜的生物合成Monoterpenoid biosynthesis | ko00902 | 48 |
25 | 倍半萜和三萜生物合成Sesquiterpenoid and triterpenoid biosynthesis | ko00909 | 44 |
26 | 咖啡因代谢Caffeine metabolism | ko00232 | 28 |
27 | 花青素生物合成Anthocyanin biosynthesis | ko00942 | 14 |
29 | 甜菜红碱生物合成Betalain biosynthesis | ko00965 | 10 |
30 | 异黄酮生物合成Isoflavonoid biosynthesis | ko00943 | 6 |
31 | 吲哚生物碱生物合成Indole alkaloid biosynthesis | ko00901 | 1 |
Fig.6 Lignins and flavonoids biosynthesis pathways in the leaves of P. cordata with cadmium exposure The numbers in the figure indicate multiple of differences in gene expression. Negative value-down regulated genes;positive value-up regulated genes
次生代谢物合成 Secondary metabolite biosynthesis | 处理组 Treatments | 酶 Enzyme | Unigene数量 Number of unigenes | Unigenes ID |
---|---|---|---|---|
木质素生物合成 Lignin biosynthesis | 6_0 h | 4CL | 1 | Cluster-26045.4660 |
POD | 2 | Cluster-26045.77742、Cluster-26045.12955 | ||
CAD | 1 | Cluster-26045.148350 | ||
48_0 h | C4H | 3 | Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.80533 | |
CSE | 1 | Cluster-26045.85997 | ||
48_6 h | PAL | 2 | Cluster-26045.2673、Cluster-26045.24951 | |
C4H | 6 | Cluster-26045.95506、Cluster-26045.151320、Cluster-26045.75438、 Cluster-26045.75436、Cluster-26045.80533、Cluster-26045.80534 | ||
4CL | 4 | Cluster-26045.55726、Cluster-26045.4660、Cluster-26045.165138、 Cluster-26045.184072 | ||
CSE | 1 | Cluster-26045.85997 | ||
CCoAOMT | 1 | Cluster-26045.92307 | ||
黄酮类生物合成 Flavonoids biosynthesis | 6_0 h | F3H | 1 | Cluster-26045.99470 |
48_0 h | C4H | 3 | Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.80533 | |
F3' 5'H | 1 | Cluster-26045.129615 | ||
F3OMT | 1 | Cluster-26045.149659 | ||
48_6 h | C4H | 6 | Cluster-26045.95506、Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.75436、Cluster-26045.80533、Cluster-26045.80534 | |
CCoAOMT | 1 | Cluster-26045.92307 | ||
ANS | 1 | Cluster-26045.156185 | ||
3GT | 3 | Cluster-26045.95421、Cluster-26045.98852、Cluster-26045.98851 | ||
I2’H | 1 | Cluster-26045.87175 |
Table 4 Unigenes enconding enzyme involved in lignin and flavonoid biosynthesis in the leaves of P. cordata with cadmium exposure
次生代谢物合成 Secondary metabolite biosynthesis | 处理组 Treatments | 酶 Enzyme | Unigene数量 Number of unigenes | Unigenes ID |
---|---|---|---|---|
木质素生物合成 Lignin biosynthesis | 6_0 h | 4CL | 1 | Cluster-26045.4660 |
POD | 2 | Cluster-26045.77742、Cluster-26045.12955 | ||
CAD | 1 | Cluster-26045.148350 | ||
48_0 h | C4H | 3 | Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.80533 | |
CSE | 1 | Cluster-26045.85997 | ||
48_6 h | PAL | 2 | Cluster-26045.2673、Cluster-26045.24951 | |
C4H | 6 | Cluster-26045.95506、Cluster-26045.151320、Cluster-26045.75438、 Cluster-26045.75436、Cluster-26045.80533、Cluster-26045.80534 | ||
4CL | 4 | Cluster-26045.55726、Cluster-26045.4660、Cluster-26045.165138、 Cluster-26045.184072 | ||
CSE | 1 | Cluster-26045.85997 | ||
CCoAOMT | 1 | Cluster-26045.92307 | ||
黄酮类生物合成 Flavonoids biosynthesis | 6_0 h | F3H | 1 | Cluster-26045.99470 |
48_0 h | C4H | 3 | Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.80533 | |
F3' 5'H | 1 | Cluster-26045.129615 | ||
F3OMT | 1 | Cluster-26045.149659 | ||
48_6 h | C4H | 6 | Cluster-26045.95506、Cluster-26045.151320、Cluster-26045.75438、Cluster-26045.75436、Cluster-26045.80533、Cluster-26045.80534 | |
CCoAOMT | 1 | Cluster-26045.92307 | ||
ANS | 1 | Cluster-26045.156185 | ||
3GT | 3 | Cluster-26045.95421、Cluster-26045.98852、Cluster-26045.98851 | ||
I2’H | 1 | Cluster-26045.87175 |
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