Chinese Bulletin of Botany ›› 2019, Vol. 54 ›› Issue (6): 733-743.DOI: 10.11983/CBB18235
• EXPERIMENTAL COMMUNICATIONS • Previous Articles Next Articles
Na Zhang1,2,Xiuxia Liu1,Xuesen Chen1,*(
),Shujing Wu1,*()
HomeReceived:2018-11-04
Accepted:2019-02-11
Online:2019-11-01
Published:2020-07-09
Contact:
Xuesen Chen,Shujing Wu
Na Zhang,Xiuxia Liu,Xuesen Chen,Shujing Wu. Identifying Genes Responsive to Jasmonates in Apple Based on Transcriptome Analysis[J]. Chinese Bulletin of Botany, 2019, 54(6): 733-743.
| Sample | Total reads | Total base pairs | Total mapped reads | Perfect match | Mismatch | Unique match | Muti-position match | Total unmapped reads |
|---|---|---|---|---|---|---|---|---|
| CTRL1 | 15336268 (100.00%) | 751477132 (100.00%) | 10932142 (71.28%) | 6783455 (44.23%) | 4148687 (27.05%) | 9149425 (59.66%) | 1782717 (11.62%) | 4404126 (28.72%) |
| MeJA | 15339040 (100.00%) | 751612960 (100.00%) | 11052987 (72.06%) | 6921067 (45.12%) | 4131920 (26.94%) | 9177064 (59.83%) | 1875923 (12.23%) | 4286053 (27.94%) |
Table 1 The alignment result of genome sequences between sample (Gala) and Golden Delicious apple
| Sample | Total reads | Total base pairs | Total mapped reads | Perfect match | Mismatch | Unique match | Muti-position match | Total unmapped reads |
|---|---|---|---|---|---|---|---|---|
| CTRL1 | 15336268 (100.00%) | 751477132 (100.00%) | 10932142 (71.28%) | 6783455 (44.23%) | 4148687 (27.05%) | 9149425 (59.66%) | 1782717 (11.62%) | 4404126 (28.72%) |
| MeJA | 15339040 (100.00%) | 751612960 (100.00%) | 11052987 (72.06%) | 6921067 (45.12%) | 4131920 (26.94%) | 9177064 (59.83%) | 1875923 (12.23%) | 4286053 (27.94%) |
Figure 1 The screening of differentially expressed genes in leaves of apple treated by MeJA (A) Gene expression level. X-axis represents log10 (gene expression level of CTRL1), Y-axis represents log10 (gene expression level of MeJA) (The orange triangle represents up-regulated genes, the blue block represents down-regu- lated genes, and the brown dot represents no significant difference genes); (B) Differentially expressed genes. Up: Up-regulated genes; No: No significant difference genes; Down: Down-regulated genes
Figure 2 GO functional classification (A) and KEGG enrichment classification (B) of differentially expressed genes in apple leaves under MeJA treatment
| Gene ID | Log2 ratio (MeJA/CTRL1) | KEGG orthology | Blast nr | Pathway |
|---|---|---|---|---|
| MDP0000702120 | 12.32 | K14181 | (-)-alpha-pinene synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000205617 | 7.28 | K14181 | Putative pinene synthase | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000919962 | 6.57 | K14181 | (-)-alpha-pinene synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000225361 | 3.72 | K14181 | (-)-germacrene D synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000248152 | 3.24 | K14181 | (-)-germacrene D synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000692178 | 12.12 | K00517 | Cytochrome P450 82G1-like | Flavonoid biosynthesis |
| MDP0000503940 | 4.67 | K05277 | Protein SRG1-like | Flavonoid biosynthesis |
| MDP0000225939 | 3.55 | K05277 | Flavonol synthase/flavanone 3-hydroxylase-like | Flavonoid biosynthesis |
| MDP0000523477 | -3.17 | K01859 | Chalcone-flavonone isomerase-like isoform X5 | Flavonoid biosynthesis |
| MDP0000317152 | 13.53 | K13407 | Cytochrome P450 94C1-like | Cutin, suberine and wax biosynthesis |
| MDP0000153822 | 3.25 | K13407 | Cytochrome P450 94B3-like | Cutin, suberine and wax biosynthesis |
| MDP0000218691 | 3.89 | K01183 | Acidic endochitinase-like | Amino sugar and nucleotide sugar metabolism |
| MDP0000280265 | 3.22 | K01183 | Acidic endochitinase-like | Amino sugar and nucleotide sugar metabolism |
| MDP0000687619 | 12.96 | K09755 | Cytochrome P450 CYP736A12-like | Phenylpropanoid biosynthesis |
| MDP0000539956 | 3.9 | K09755 | Cytochrome P450 CYP736A12-like | Phenylpropanoid biosynthesis |
| MDP0000313394 | 6.44 | K13267 | Cytochrome P450 CYP736A12-like | Isoflavonoid biosynthesis |
| MDP0000813805 | -6.29 | K09840 | 9-cis-epoxycarotenoid dioxygenase NCED3, chloroplastic-like | Carotenoid biosynthesis |
| MDP0000228070 | -5.24 | K09840 | 9-cis-epoxycarotenoid dioxygenase NCED1, chloroplastic-like | Carotenoid biosynthesis |
| Gene ID | Log2 ratio (MeJA/CTRL1) | KEGG orthology | Blast nr | Pathway |
|---|---|---|---|---|
| MDP0000702120 | 12.32 | K14181 | (-)-alpha-pinene synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000205617 | 7.28 | K14181 | Putative pinene synthase | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000919962 | 6.57 | K14181 | (-)-alpha-pinene synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000225361 | 3.72 | K14181 | (-)-germacrene D synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000248152 | 3.24 | K14181 | (-)-germacrene D synthase-like | Sesquiterpenoid and triterpenoid biosynthesis |
| MDP0000692178 | 12.12 | K00517 | Cytochrome P450 82G1-like | Flavonoid biosynthesis |
| MDP0000503940 | 4.67 | K05277 | Protein SRG1-like | Flavonoid biosynthesis |
| MDP0000225939 | 3.55 | K05277 | Flavonol synthase/flavanone 3-hydroxylase-like | Flavonoid biosynthesis |
| MDP0000523477 | -3.17 | K01859 | Chalcone-flavonone isomerase-like isoform X5 | Flavonoid biosynthesis |
| MDP0000317152 | 13.53 | K13407 | Cytochrome P450 94C1-like | Cutin, suberine and wax biosynthesis |
| MDP0000153822 | 3.25 | K13407 | Cytochrome P450 94B3-like | Cutin, suberine and wax biosynthesis |
| MDP0000218691 | 3.89 | K01183 | Acidic endochitinase-like | Amino sugar and nucleotide sugar metabolism |
| MDP0000280265 | 3.22 | K01183 | Acidic endochitinase-like | Amino sugar and nucleotide sugar metabolism |
| MDP0000687619 | 12.96 | K09755 | Cytochrome P450 CYP736A12-like | Phenylpropanoid biosynthesis |
| MDP0000539956 | 3.9 | K09755 | Cytochrome P450 CYP736A12-like | Phenylpropanoid biosynthesis |
| MDP0000313394 | 6.44 | K13267 | Cytochrome P450 CYP736A12-like | Isoflavonoid biosynthesis |
| MDP0000813805 | -6.29 | K09840 | 9-cis-epoxycarotenoid dioxygenase NCED3, chloroplastic-like | Carotenoid biosynthesis |
| MDP0000228070 | -5.24 | K09840 | 9-cis-epoxycarotenoid dioxygenase NCED1, chloroplastic-like | Carotenoid biosynthesis |
Figure 3 Effect of MeJA on plant hormone signaling pathways in leaves of apple on the right side of red frame: Up-regulated; on the right side of green frame: Down-regulated; on the right side of red-green frame: Include both up-regulated and down-regulated genes.
| Plant hormone signaling pathway | Gene ID | Log2 ratio (MeJA/CTRL1) |
|---|---|---|
| Auxin | MDP0000300452 | -1.4 |
| MDP0000255223 MDP0000213864 | 1.1 -1.1 | |
| MDP0000143749 MDP0000221322 | 1.3 -1.6 | |
| MDP0000873893 MDP0000214081 | 1.5 -1.1 | |
| MDP0000786165 | 1.1 | |
| Cytokinine | MDP0000146863 | -1.1 |
| MDP0000285242 MDP0000225179 | 1.6 -1.0 | |
| MDP0000250737 | -1.5 | |
| Gibberellin | MDP0000227827 MDP0000868088 | -1.3 -1.0 |
| MDP0000284679 MDP0000227056 MDP0000397638 | 1.4 1.3 -2.2 | |
| Abscisic acid | MDP0000437033 MDP0000203818 MDP0000283274 | -1.6 -1.3 -1.2 |
| Ethylene | MDP0000275915 | -2.4 |
| MDP0000855671 MDP0000127134 MDP0000235313 MDP0000805422 MDP0000787281 | 3.1 2.5 1.8 1.2 1.0 | |
| Brassinosteroid | MDP0000123379 MDP0000319460 MDP0000319708 MDP0000904826 MDP0000196862 | 12.5 1.9 1.0 1.0 -1.8 |
| MDP0000217213 MDP0000897962 MDP0000290950 MDP0000620422 MDP0000303744 MDP0000189315 MDP0000741253 MDP0000223726 MDP0000189841 | 1.9 1.3 -2.3 -1.8 -1.6 -1.1 -1.0 -1.0 -1.0 | |
| MDP0000130143 | -12.8 | |
| MDP0000320017 | -1.4 | |
| MDP0000135392 | -1.0 | |
| Jasmonic acid | MDP0000565690 MDP0000187921 MDP0000889413 MDP0000301927 | 2.8 2.6 1.7 1.2 |
| MDP0000603546 MDP0000242554 MDP0000029168 MDP0000900024 MDP0000226497 MDP0000290263 | 3.6 2.2 1.6 1.6 1.0 -1.0 | |
| Salicylic acid | MDP0000292425 | 1.8 |
| MDP0000529682 MDP0000375992 | 1.1 -4.3 |
Table 3 The significant differentially expressed genes involved in plant hormone signaling in leaves of apple under MeJA treatment
| Plant hormone signaling pathway | Gene ID | Log2 ratio (MeJA/CTRL1) |
|---|---|---|
| Auxin | MDP0000300452 | -1.4 |
| MDP0000255223 MDP0000213864 | 1.1 -1.1 | |
| MDP0000143749 MDP0000221322 | 1.3 -1.6 | |
| MDP0000873893 MDP0000214081 | 1.5 -1.1 | |
| MDP0000786165 | 1.1 | |
| Cytokinine | MDP0000146863 | -1.1 |
| MDP0000285242 MDP0000225179 | 1.6 -1.0 | |
| MDP0000250737 | -1.5 | |
| Gibberellin | MDP0000227827 MDP0000868088 | -1.3 -1.0 |
| MDP0000284679 MDP0000227056 MDP0000397638 | 1.4 1.3 -2.2 | |
| Abscisic acid | MDP0000437033 MDP0000203818 MDP0000283274 | -1.6 -1.3 -1.2 |
| Ethylene | MDP0000275915 | -2.4 |
| MDP0000855671 MDP0000127134 MDP0000235313 MDP0000805422 MDP0000787281 | 3.1 2.5 1.8 1.2 1.0 | |
| Brassinosteroid | MDP0000123379 MDP0000319460 MDP0000319708 MDP0000904826 MDP0000196862 | 12.5 1.9 1.0 1.0 -1.8 |
| MDP0000217213 MDP0000897962 MDP0000290950 MDP0000620422 MDP0000303744 MDP0000189315 MDP0000741253 MDP0000223726 MDP0000189841 | 1.9 1.3 -2.3 -1.8 -1.6 -1.1 -1.0 -1.0 -1.0 | |
| MDP0000130143 | -12.8 | |
| MDP0000320017 | -1.4 | |
| MDP0000135392 | -1.0 | |
| Jasmonic acid | MDP0000565690 MDP0000187921 MDP0000889413 MDP0000301927 | 2.8 2.6 1.7 1.2 |
| MDP0000603546 MDP0000242554 MDP0000029168 MDP0000900024 MDP0000226497 MDP0000290263 | 3.6 2.2 1.6 1.6 1.0 -1.0 | |
| Salicylic acid | MDP0000292425 | 1.8 |
| MDP0000529682 MDP0000375992 | 1.1 -4.3 |
| Gene ID | Log2 ratio (MeJA/CTRL) | Annotation |
|---|---|---|
| MDP0000123379 | 12.46 | Putative serine/threonine- protein kinase |
| MDP0000603546 | 3.56 | Transcription factor MYC2- like |
| MDP0000855671 | 3.1 | Ethylene-responsive transcription factor 1B-like |
| MDP0000130143 | -12.82 | Probable serine/threonine- protein kinase At5g41260 |
| MDP0000375992 | -4.27 | U-box domain-containing protein 19-like |
Table 4 The regulated genes involved in biosynthesis of secondary metabolites pathway in leaves of apple under MeJA treatment (Log2 (MeJA/CTRL)≥3)
| Gene ID | Log2 ratio (MeJA/CTRL) | Annotation |
|---|---|---|
| MDP0000123379 | 12.46 | Putative serine/threonine- protein kinase |
| MDP0000603546 | 3.56 | Transcription factor MYC2- like |
| MDP0000855671 | 3.1 | Ethylene-responsive transcription factor 1B-like |
| MDP0000130143 | -12.82 | Probable serine/threonine- protein kinase At5g41260 |
| MDP0000375992 | -4.27 | U-box domain-containing protein 19-like |
Figure 4 Effect of MeJA on plant-pathogen interaction pathway in leaves of apple on the right side of red frame: Up-regulated; on the right side of green frame: Down-regulated; on the right side of red-green frame: Include both up-regulated and down-regulated genes.
Figure 5 qRT-PCR analysis of differentially expressed genes in leaves of apple under MeJA treatment
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