Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (2): 83-94.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0664
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PENG Guo-ying1(), HU Liang1, HUANG Chao2, YANG Kun1, WAN Wei1, HUANG Chang-gan1()
Received:
2021-05-21
Online:
2022-02-26
Published:
2022-03-09
Contact:
HUANG Chang-gan
E-mail:1114755190@qq.com;windhcg@163.com
PENG Guo-ying, HU Liang, HUANG Chao, YANG Kun, WAN Wei, HUANG Chang-gan. Transcriptome Analysis of Response to Heavy Metal Copper Stress in Setcreasea purpurea Root Tissue[J]. Biotechnology Bulletin, 2022, 38(2): 83-94.
序列号Unigene ID | 注释Annotated | 序列Sequence(5'-3') | Tm/℃ | 长度Length/bp |
---|---|---|---|---|
c1920_g1 | 磷酸化酶Phosphorylase | F:ATGTGGGCTCTGTCGTT R:TGCCTGCTGTGCTAATG | 58/60 | 178 |
c48219_g1 | 羧酸酯酶12 Carboxylesterase 12 | F:TTTGCGAGGTTGGGTAT R:AAGAGTGGCCGAGTTGA | 60/60 | 191 |
c1055_g1 | 铁通透酶基因1 Fe transporter permease 1 | F:TACCTGCCCGCCGTGTT R:TGATGACTGCCGCCTCC | 60/59 | 154 |
c1246_g1 | 金属尼古丁胺转运蛋白9 Metal nicotine amine transporter 9 | F:ATGTTAGAGTGAGATACCCTGT R:AATGGTTATGGCGTTGG | 60/60 | 177 |
c1178_g1 | 磷酸酯酶2C Protein phosphatase 2C | F:ATTACCTACGAGGAGCG R:CCAACCTTATCCCACAG | 58/60 | 164 |
c51710_g1 | 谷胱甘肽转移酶 Glutathione transferase | F:GAGCAAAGTAGGCATCG R:ACTAACGGCTTGAGGGT | 59/60 | 158 |
c18811_g1 | 生长素结合蛋白 Auxin binding protein | F:GCACTGGGTCTGCCTGAT R:TGGAGTTCGCCGATGAG | 56/60 | 146 |
c2112_g1 | 硝酸根转运蛋白 Nitrate transporter | F:CAAAGCCAACATAATACAAG R:TTGGGAGACTGAGAAGGT | 60/58 | 168 |
c30939_g1 | 水通道蛋白 Aquaporin | F:ACCCTTCTGGCTTAGTG R:AATGATGGTGATGTGGC | 57/60 | 121 |
c113_g1 | 假定蛋白21 Hypothetical protein 21 | F:GGCTCTTTCTGGCTCGTA R:CAAGTTCATTGGCACCC | 56/60 | 138 |
Table 1 Primer sequence of qRT-PCR
序列号Unigene ID | 注释Annotated | 序列Sequence(5'-3') | Tm/℃ | 长度Length/bp |
---|---|---|---|---|
c1920_g1 | 磷酸化酶Phosphorylase | F:ATGTGGGCTCTGTCGTT R:TGCCTGCTGTGCTAATG | 58/60 | 178 |
c48219_g1 | 羧酸酯酶12 Carboxylesterase 12 | F:TTTGCGAGGTTGGGTAT R:AAGAGTGGCCGAGTTGA | 60/60 | 191 |
c1055_g1 | 铁通透酶基因1 Fe transporter permease 1 | F:TACCTGCCCGCCGTGTT R:TGATGACTGCCGCCTCC | 60/59 | 154 |
c1246_g1 | 金属尼古丁胺转运蛋白9 Metal nicotine amine transporter 9 | F:ATGTTAGAGTGAGATACCCTGT R:AATGGTTATGGCGTTGG | 60/60 | 177 |
c1178_g1 | 磷酸酯酶2C Protein phosphatase 2C | F:ATTACCTACGAGGAGCG R:CCAACCTTATCCCACAG | 58/60 | 164 |
c51710_g1 | 谷胱甘肽转移酶 Glutathione transferase | F:GAGCAAAGTAGGCATCG R:ACTAACGGCTTGAGGGT | 59/60 | 158 |
c18811_g1 | 生长素结合蛋白 Auxin binding protein | F:GCACTGGGTCTGCCTGAT R:TGGAGTTCGCCGATGAG | 56/60 | 146 |
c2112_g1 | 硝酸根转运蛋白 Nitrate transporter | F:CAAAGCCAACATAATACAAG R:TTGGGAGACTGAGAAGGT | 60/58 | 168 |
c30939_g1 | 水通道蛋白 Aquaporin | F:ACCCTTCTGGCTTAGTG R:AATGATGGTGATGTGGC | 57/60 | 121 |
c113_g1 | 假定蛋白21 Hypothetical protein 21 | F:GGCTCTTTCTGGCTCGTA R:CAAGTTCATTGGCACCC | 56/60 | 138 |
样本 Sample | 原始数据 Raw reads/Mb | 过滤数据 Clean reads /Mb | 碱基总数 Total number of bases/Gb | Q20/% | Q30/% | 过滤数据率 Clean reads ratio/% |
---|---|---|---|---|---|---|
CK-1 | 46.39 | 42.94 | 7.00 | 96.91 | 92.50 | 92.58 |
CK-2 | 44.77 | 41.86 | 6.76 | 96.86 | 92.44 | 93.51 |
CK-3 | 43.28 | 40.72 | 6.54 | 96.88 | 92.36 | 94.07 |
CT1-1 | 44.58 | 41.71 | 6.73 | 96.82 | 92.34 | 93.56 |
CT1-2 | 50.21 | 47.17 | 7.58 | 96.89 | 92.36 | 93.95 |
CT1-3 | 44.60 | 41.94 | 6.73 | 96.67 | 91.91 | 94.03 |
CT2-1 | 47.85 | 44.95 | 7.23 | 96.79 | 92.17 | 93.93 |
CT2-2 | 40.67 | 38.21 | 6.14 | 96.92 | 92.43 | 93.95 |
CT2-3 | 45.70 | 42.69 | 6.90 | 96.91 | 92.42 | 93.40 |
Table 2 Data statistics of disembarkation
样本 Sample | 原始数据 Raw reads/Mb | 过滤数据 Clean reads /Mb | 碱基总数 Total number of bases/Gb | Q20/% | Q30/% | 过滤数据率 Clean reads ratio/% |
---|---|---|---|---|---|---|
CK-1 | 46.39 | 42.94 | 7.00 | 96.91 | 92.50 | 92.58 |
CK-2 | 44.77 | 41.86 | 6.76 | 96.86 | 92.44 | 93.51 |
CK-3 | 43.28 | 40.72 | 6.54 | 96.88 | 92.36 | 94.07 |
CT1-1 | 44.58 | 41.71 | 6.73 | 96.82 | 92.34 | 93.56 |
CT1-2 | 50.21 | 47.17 | 7.58 | 96.89 | 92.36 | 93.95 |
CT1-3 | 44.60 | 41.94 | 6.73 | 96.67 | 91.91 | 94.03 |
CT2-1 | 47.85 | 44.95 | 7.23 | 96.79 | 92.17 | 93.93 |
CT2-2 | 40.67 | 38.21 | 6.14 | 96.92 | 92.43 | 93.95 |
CT2-3 | 45.70 | 42.69 | 6.90 | 96.91 | 92.42 | 93.40 |
数据库 Database | 注释基因的数量Number of annotated unigenes | 注释基因的比例Percentage of annotated unigenes/% |
---|---|---|
NR | 68 227 | 82.73 |
GO | 23 236 | 28.17 |
KEGG | 35 123 | 42.59 |
Pfam | 27 806 | 33.72 |
eggNOG | 67 602 | 81.97 |
Swissprot | 52 994 | 64.26 |
In all database | 8 422 | 10.21 |
Table 3 Summary of database annotation results
数据库 Database | 注释基因的数量Number of annotated unigenes | 注释基因的比例Percentage of annotated unigenes/% |
---|---|---|
NR | 68 227 | 82.73 |
GO | 23 236 | 28.17 |
KEGG | 35 123 | 42.59 |
Pfam | 27 806 | 33.72 |
eggNOG | 67 602 | 81.97 |
Swissprot | 52 994 | 64.26 |
In all database | 8 422 | 10.21 |
对照组Control | 实验组Case | 上调基因数Number of up-regulated gene | 下调基因数Number of down-regulated gene | 差异表达基因总数Total DEGs |
---|---|---|---|---|
CK | CT1 | 3 138 | 1 890 | 5 028 |
CK | CT2 | 5 061 | 4 921 | 9 982 |
CT1 | CT2 | 2 555 | 4 258 | 6 813 |
Table 4 Statistical analysis of differentially expressed genes in S. purpurea roots
对照组Control | 实验组Case | 上调基因数Number of up-regulated gene | 下调基因数Number of down-regulated gene | 差异表达基因总数Total DEGs |
---|---|---|---|---|
CK | CT1 | 3 138 | 1 890 | 5 028 |
CK | CT2 | 5 061 | 4 921 | 9 982 |
CT1 | CT2 | 2 555 | 4 258 | 6 813 |
Fig. 2 Volcano map of differentially expressed genes The blue dot region on the left refers to significantly down-regulated genes,the red dot region on the right refers to significantly up-regulated genes,and the gray dot region on the bottom refers to non-significantly differentially expressed gene
KEGG ID | 注释 Annotated | 上调基因数 Number of up-regulated genes | 下调基因数Number of down-regulated genes | 差异表达基因总数 Total DEGs | P值 P value | |
---|---|---|---|---|---|---|
CT1 vs CK | ko00940 | 类苯基丙酸合成 Phenylpropanoid biosynthesis | 78 | 21 | 99 | 1.902E-30 |
ko00500 | 淀粉和蔗糖代谢 Starch and sucrose metabolism | 54 | 30 | 84 | 1.265E-15 | |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 31 | 1 | 32 | 1.298E-13 | |
CT2 vs CT1 | ko04016 | 植物MAPK信号通路 Plant MAPK signaling pathway | 89 | 84 | 173 | 3.056E-26 |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 62 | 82 | 144 | 5.213E-23 | |
ko04146 | 过氧物酶体 Peroxisome | 65 | 106 | 171 | 2.283E-17 |
Table 5 The significant KEGG enrichment pathway in S. purpurea transcriptome
KEGG ID | 注释 Annotated | 上调基因数 Number of up-regulated genes | 下调基因数Number of down-regulated genes | 差异表达基因总数 Total DEGs | P值 P value | |
---|---|---|---|---|---|---|
CT1 vs CK | ko00940 | 类苯基丙酸合成 Phenylpropanoid biosynthesis | 78 | 21 | 99 | 1.902E-30 |
ko00500 | 淀粉和蔗糖代谢 Starch and sucrose metabolism | 54 | 30 | 84 | 1.265E-15 | |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 31 | 1 | 32 | 1.298E-13 | |
CT2 vs CT1 | ko04016 | 植物MAPK信号通路 Plant MAPK signaling pathway | 89 | 84 | 173 | 3.056E-26 |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 62 | 82 | 144 | 5.213E-23 | |
ko04146 | 过氧物酶体 Peroxisome | 65 | 106 | 171 | 2.283E-17 |
基因序列号Unigene ID | 注释 Annotated | RNA-seq | |||||
---|---|---|---|---|---|---|---|
Log2FC(CT1/CK) | P值P-value | Log2FC(CT2/CK) | P值P value | ||||
c76816_g1 | 重金属转运ATP酶5 Heavy metal transporting ATPase 5,HMA5 | 1.61 | 3.122E-05 | 0.97 | 1.502E-06 | ||
c34452_g1 | 谷胱甘肽过氧化物酶Glutathione peroxidase,GPX | 2.95 | 1.521E-08 | 4.12 | 3.830E-07 | ||
c14543_g1 | 铜锌超氧化物歧化酶 Cu/Zn superoxide dismutase,Cu/Zn-SOD | 1.22 | 0.000442 | 1.08 | 0.000131 | ||
c11849_g1 | 金属硫蛋白Metallothioneins,MTs | 1.67 | 0.000924 | 3.37 | 0.000210 | ||
c44409_g1 | 植物络合素合酶Phytochelatin synthase,PCS | 0.49 | 0.000148 | 1.21 | 0.000251 |
Table 6 Analysis of genes related to copper stress
基因序列号Unigene ID | 注释 Annotated | RNA-seq | |||||
---|---|---|---|---|---|---|---|
Log2FC(CT1/CK) | P值P-value | Log2FC(CT2/CK) | P值P value | ||||
c76816_g1 | 重金属转运ATP酶5 Heavy metal transporting ATPase 5,HMA5 | 1.61 | 3.122E-05 | 0.97 | 1.502E-06 | ||
c34452_g1 | 谷胱甘肽过氧化物酶Glutathione peroxidase,GPX | 2.95 | 1.521E-08 | 4.12 | 3.830E-07 | ||
c14543_g1 | 铜锌超氧化物歧化酶 Cu/Zn superoxide dismutase,Cu/Zn-SOD | 1.22 | 0.000442 | 1.08 | 0.000131 | ||
c11849_g1 | 金属硫蛋白Metallothioneins,MTs | 1.67 | 0.000924 | 3.37 | 0.000210 | ||
c44409_g1 | 植物络合素合酶Phytochelatin synthase,PCS | 0.49 | 0.000148 | 1.21 | 0.000251 |
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