Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (5): 233-242.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1241
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SHI Jian-lei1,2(), ZAI Wen-shan1, SU Shi-wen1, FU Cun-nian1, XIONG Zi-li1()
Received:
2022-10-09
Online:
2023-05-26
Published:
2023-06-08
Contact:
XIONG Zi-li
E-mail:sjlhebau@163.com;273493129@qq.com
SHI Jian-lei, ZAI Wen-shan, SU Shi-wen, FU Cun-nian, XIONG Zi-li. Identification and Expression Analysis of miRNA Related to Bacterial Wilt Resistance in Tomato[J]. Biotechnology Bulletin, 2023, 39(5): 233-242.
基因 Gene | 序列 Sequence(5'-3') | 引物 Primer(5'-3') |
---|---|---|
SlU6 | GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCACAAATCGAGAAATGGTCCAAAATTTT | F: GGGACATCCGATAAAATTGG R: TTGGACCATTTCTCGATTTGT |
novel_miR_13 | GGCGGAUGUAGCCAAGUGGA | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCACTT F: ACACTCCAGCTGGGGGCGGATGTAGCC |
sly-miR172c | AGAATCTTGATGATGCTGCAG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGAGAATCTTGATGAT |
sly-miR172d | GGAATCTTGATGATGCTGCAG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGGGAATCTTGATGAT |
sly-miR396a-5p | TTCCACAGCTTTCTTGAACTG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCAGTTCAA F: ACACTCCAGCTGGGTTCCACAGCTTTC |
All R: TGGTGTCGTGGAGTCG |
Table 1 Primers used for RT-qPCR
基因 Gene | 序列 Sequence(5'-3') | 引物 Primer(5'-3') |
---|---|---|
SlU6 | GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCACAAATCGAGAAATGGTCCAAAATTTT | F: GGGACATCCGATAAAATTGG R: TTGGACCATTTCTCGATTTGT |
novel_miR_13 | GGCGGAUGUAGCCAAGUGGA | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCACTT F: ACACTCCAGCTGGGGGCGGATGTAGCC |
sly-miR172c | AGAATCTTGATGATGCTGCAG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGAGAATCTTGATGAT |
sly-miR172d | GGAATCTTGATGATGCTGCAG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGGGAATCTTGATGAT |
sly-miR396a-5p | TTCCACAGCTTTCTTGAACTG | RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCAGTTCAA F: ACACTCCAGCTGGGTTCCACAGCTTTC |
All R: TGGTGTCGTGGAGTCG |
样本Library | 净读数Clean reads/M | 净碱基数Clean bases/Gb | GC含量GC content/% | Q30/% | 无注释Unannotated | 比对读数Mapped reads |
---|---|---|---|---|---|---|
RC02 | 14.31 | 0.32 | 41.86 | 95.26 | 10.81 | 7.08 |
RC14 | 16.69 | 0.38 | 42.34 | 95.26 | 11.86 | 7.68 |
RT06 | 12.93 | 0.30 | 42.68 | 95.61 | 8.85 | 5.72 |
RT18 | 10.84 | 0.24 | 41.95 | 95.57 | 7.92 | 5.11 |
SC04 | 14.57 | 0.33 | 42.10 | 95.68 | 10.22 | 7.31 |
SC16 | 16.54 | 0.37 | 43.15 | 95.75 | 10.79 | 7.77 |
ST08 | 11.32 | 0.26 | 42.76 | 95.55 | 7.68 | 5.14 |
ST20 | 15.56 | 0.35 | 41.62 | 95.77 | 11.52 | 7.75 |
Table 2 Statistics of sRNA sequencing reads in the eight tomato libraries
样本Library | 净读数Clean reads/M | 净碱基数Clean bases/Gb | GC含量GC content/% | Q30/% | 无注释Unannotated | 比对读数Mapped reads |
---|---|---|---|---|---|---|
RC02 | 14.31 | 0.32 | 41.86 | 95.26 | 10.81 | 7.08 |
RC14 | 16.69 | 0.38 | 42.34 | 95.26 | 11.86 | 7.68 |
RT06 | 12.93 | 0.30 | 42.68 | 95.61 | 8.85 | 5.72 |
RT18 | 10.84 | 0.24 | 41.95 | 95.57 | 7.92 | 5.11 |
SC04 | 14.57 | 0.33 | 42.10 | 95.68 | 10.22 | 7.31 |
SC16 | 16.54 | 0.37 | 43.15 | 95.75 | 10.79 | 7.77 |
ST08 | 11.32 | 0.26 | 42.76 | 95.55 | 7.68 | 5.14 |
ST20 | 15.56 | 0.35 | 41.62 | 95.77 | 11.52 | 7.75 |
样本 Library | 已知miRNA Known miRNA | 新miRNA Novel miRNA | 总数 Total | 新miRNA百分率 Novel miRNA percentage/% |
---|---|---|---|---|
RC02 | 134 | 193 | 327 | 59.02 |
RC14 | 138 | 193 | 331 | 58.31 |
RT06 | 136 | 192 | 328 | 58.54 |
RT18 | 132 | 190 | 322 | 59.01 |
SC04 | 137 | 193 | 330 | 58.48 |
SC16 | 136 | 193 | 329 | 58.66 |
ST08 | 134 | 193 | 327 | 59.02 |
ST20 | 136 | 193 | 329 | 58.66 |
Total | 143 | 193 | 336 | 57.44 |
Table 3 Statistics of known and new miRNA in each lib-rary
样本 Library | 已知miRNA Known miRNA | 新miRNA Novel miRNA | 总数 Total | 新miRNA百分率 Novel miRNA percentage/% |
---|---|---|---|---|
RC02 | 134 | 193 | 327 | 59.02 |
RC14 | 138 | 193 | 331 | 58.31 |
RT06 | 136 | 192 | 328 | 58.54 |
RT18 | 132 | 190 | 322 | 59.01 |
SC04 | 137 | 193 | 330 | 58.48 |
SC16 | 136 | 193 | 329 | 58.66 |
ST08 | 134 | 193 | 327 | 59.02 |
ST20 | 136 | 193 | 329 | 58.66 |
Total | 143 | 193 | 336 | 57.44 |
Fig. 1 Differentially expressed miRNA in resistance and susceptible tomato lines Up and Down indicate up-regulated and down-regulated expression, respectively
类型 Type | 所有miRNA All miRNA | 具有靶基因的miRNA miRNA with targets | 靶基因 Target genes |
---|---|---|---|
Known miRNA | 143 | 134 | 2 268 |
Novel miRNA | 193 | 159 | 1 943 |
总数 Total | 336 | 293 | 3 960 |
Table 4 Statistics of miRNA targets
类型 Type | 所有miRNA All miRNA | 具有靶基因的miRNA miRNA with targets | 靶基因 Target genes |
---|---|---|---|
Known miRNA | 143 | 134 | 2 268 |
Novel miRNA | 193 | 159 | 1 943 |
总数 Total | 336 | 293 | 3 960 |
Fig. 5 Relative expressions of ten selected miRNA-targets in resistant and susceptible tomato lines with R. solanacearum infection R and S represent resistant and susceptible tomato lines, respectively. * and ** indicate statistically significant differences (P < 0.05 and P < 0.01). SD stands for standard deviation. A: 1: novel_miR_13; 2: Solyc09g091370.4. B:1: sly-miR396a-5p; 2: Solyc02g032870.4; 3: Solyc07g041640.3; 4: Solyc09g009200.3. C: 1: sly-miR172c; 2: Solyc04g064620.4; 3: Solyc10g006710.4; 4: Solyc12g099450.3. D: 1: sly-miR172d; 2: Solyc09g075550.3; 3: Solyc10g006710.4; 4: Solyc12g099450.3
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