Comparative Transcriptomic Analysis of Clove Basil （Ocimum gratissimum） Leaves in Response to Cadmium Stress

doi:10.13560/j.cnki.biotech.bull.1985.2024-0618

Abstract

Abstract:

Objective Clove basil (Ocimum gratissimum) has the potential for both remediation and safe utilization of cadmium (Cd)-contaminated soil. Elucidating the molecular mechanisms of clove basil in response to Cd stress and identifying key regulatory factors closely associated with Cd tolerance may provide candidate gene resources for the innovation of germplasm resources of clove basil tolerant to Cd stress. Method This study employed comparative transcriptome to analyze the transcriptomic changes in clove basil leaves during 72 h of Cd treatment (35 μmol/L). Result Cd stress significantly inhibited the growth of clove basil. The leaves, stems, and roots of clove basil accumulated high levels of Cd, with the highest content in the roots. Additionally, Cd stress significantly affected the composition and content of essential oils, inducing the biosynthesis and accumulation of methyl ester cinnamic acid in the leaves. The transcriptome analysis results showed that differentially expressed genes (DEGs) were significantly enriched in pathways such as ribosome, plant-pathogen interaction, and the MAPK signaling pathway in the 24 h comparative group. Whereas DEGs were significantly enriched in pathways including photosynthesis, photosynthesis-antenna proteins, and porphyrin and chlorophyll metabolism in the 72 h comparative group. Genes within the light cyan1 module were significantly correlated with the Cd stress phenotype. These genes were primarily enriched in defense pathways such as plant hormone signal transduction, plant-pathogen interaction, and the MAPK signaling pathway. Furthermore, the upregulated DEGs in response to Cd stress were also significantly enriched in these three pathways, suggesting that the activation of these pathways was the main mechanism by which clove basil leaves responded to Cd stress. Cd stress treatment induced the expressions of 13 transcription factor genes, in which 5 genes from the bHLH family, suggesting crucial roles for bHLH transcription factors in regulating Cd stress tolerance in clove basil. Conclusion The molecular mechanisms by which clove basil responds to Cd stress closely resemble those of other plant species, and the bHLH transcription factor appears to act as key regulators of Cd tolerance in clove basil.

Key words: clove basil, cadmium stress, RNA-Seq, photosynthesis, bHLH transcription factor

WANG Bin, WANG Yu-kun, XIAO Yan-hui. Comparative Transcriptomic Analysis of Clove Basil （Ocimum gratissimum） Leaves in Response to Cadmium Stress[J]. Biotechnology Bulletin, 2025, 41(3): 255-270.

Figures/Tables 13

References 37

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基因编号 Gene ID	正向引物序列 Forward primer sequence （5΄‒3΄）	反向引物序列 Reverse primer sequence （5΄‒3΄）	产物长度 Product length/bp
c52549.graph_c0	ATCGAGCAGAGATGAAGCCG	TTGACGCGCGTGTTTTTCAT	134
c49765.graph_c0	AACAAGAGGGCGGAAGGAAG	AGAGAAAGAGGGGCTGTTGC	73
c57224.graph_c0	AAGGCGCTGGAATCGGATAG	GCGATTTGCACTCCACGTTT	125
c59334.graph_c0	CACAATTCCGATCGCACGAC	TGGCCTCCAAGTTATGCTGG	71
c51522.graph_c0	CGGTTCGTCTCCTTGGTGAA	AGTCTCCTCGACCAGCTCAT	119
c54882.graph_c1	AGGATGGTGTGAGGAGAGCA	TGCTCAAGTGGAGGATGCAA	140
Actin7	GGAGCTCGTCTTTGCTGTCT	GAGCGGGAAATTGTGAGGGA	90

基因编号 Gene ID	正向引物序列 Forward primer sequence （5΄‒3΄）	反向引物序列 Reverse primer sequence （5΄‒3΄）	产物长度 Product length/bp
c52549.graph_c0	ATCGAGCAGAGATGAAGCCG	TTGACGCGCGTGTTTTTCAT	134
c49765.graph_c0	AACAAGAGGGCGGAAGGAAG	AGAGAAAGAGGGGCTGTTGC	73
c57224.graph_c0	AAGGCGCTGGAATCGGATAG	GCGATTTGCACTCCACGTTT	125
c59334.graph_c0	CACAATTCCGATCGCACGAC	TGGCCTCCAAGTTATGCTGG	71
c51522.graph_c0	CGGTTCGTCTCCTTGGTGAA	AGTCTCCTCGACCAGCTCAT	119
c54882.graph_c1	AGGATGGTGTGAGGAGAGCA	TGCTCAAGTGGAGGATGCAA	140
Actin7	GGAGCTCGTCTTTGCTGTCT	GAGCGGGAAATTGTGAGGGA	90

序号 No.	化合物名称 Compound name	保留时间 Retention time/min	含量 Content/%		序号 No.	化合物名称 Compound name	保留时间 Retention time/min	含量 Content/%
序号 No.	化合物名称 Compound name	保留时间 Retention time/min	CK	Cd	序号 No.	化合物名称 Compound name	保留时间 Retention time/min	CK	Cd
1	3-己烯醛 3-hexenal	4.13	1.86±0.16*	0.68±0.04	26	顺式-肉桂酸甲酯 Methyl cis-cinnamate	12.00	-	5.13±0.26
2	（E）-2-己烯醛（E）-2-hexenal	4.96	0.25±0.01*	0.08±0.00	27	丁香酚Eugenol	12.71	25.7±1.41*	0.02±0.01
3	顺式-3-己烯醇 Cis-3-hexenol	5.00	1.54±0.41*	0.14±0.04	28	肉桂酸甲酯 Methyl ester cinnamic acid	13.06	0.06±0.10	58.02±2.02*
4	α-侧柏烯 α-thujene	6.16	0.15±0.02*	0.06±0.01	29	β-榄香烯 β-elemene	13.21	0.83±0.09*	0.31±0.04
5	α-蒎烯 α-pinene	6.28	0.38±0.02*	0.21±0.01	30	甲基丁香酚 Methyl eugenol	13.28	6.56±0.14*	2.04±0.31
6	莰烯 Camphene	6.54	0.06±0.01	0.02±0.00	31	β-佛手柑油烯 β-bergamotene	13.49	0.10±0.01	0.05±0.01
7	香桧烯 Sabinene	6.93	0.14±0.01*	0.08±0.01	32	石竹烯 Caryophyllene	13.64	0.31±0.02*	0.16±0.01
8	β-蒎烯β-pinene	7.00	0.38±0.04*	0.19±0.01	33	反式-α-佛手柑油烯 Trans-α-bergamotene	13.76	2.41±0.11	2.09±0.05
9	β-月桂烯 β-myrcene	7.18	0.02±0.01	0.10±0.00*	34	顺式-β-金合欢烯Cis-β-farnesene	13.83	0.21±0.02	0.08±0.02
10	D-柠檬烯 D-limonene	7.83	0.32±0.00*	0.15±0.00	35	反式-β-金合欢烯 Trans-β-farnesene	13.95	0.29±0.03*	0.19±0.02
11	桉树脑 Eucalyptol	7.89	3.02±0.11*	1.95±0.09	36	蛇麻烯 Humulene	14.08	1.27±0.04*	0.70±0.02
12	（E）-β-罗勒烯（E）-β-ocimene	8.10	2.27±0.11*	1.13±0.02	37	顺式-4（15），5-依兰油二烯 Cis-muurola-4（15），5-diene	14.18	0.25±0.05*	0.08±0.01
13	γ-松油烯 γ-terpinene	8.30	0.40±0.02*	0.14±0.01	38	大根香叶烯 D Germacrene D	14.41	2.52±0.04*	1.18±0.02
14	顺式-水合香桧烯Cis-sabinene hydrate	8.46	0.79±0.05*	0.27±0.01	39	β-环大根香叶烷 β-cyclogermacrane	14.61	1.54±0.09*	0.4±0.01
15	萜品油烯 Terpinolene	8.78	0.14±0.01*	0.01±0.02	40	δ-愈创木烯 δ-guaiene	14.69	0.21±0.02*	0.06±0.02
16	葑酮 Fenchone	8.82	0.23±0.02	0.23±0.05	41	γ-杜松烯 γ-cadinene	14.80	1.07±0.04*	0.56±0.02
17	芳樟醇 Linalool	8.92	12.10±0.51*	4.15±0.19	42	β-倍半水芹烯 β-sesquiphellandrene	14.86	0.11±0.03	0.06±0.01
18	（+）-2-莰酮（+）-2-bornanone	9.71	0.85±0.03*	0.25±0.01	43	α-杜松烯 α-cadinene	15.01	0.09±0.02	0.03±0.00
19	新薄荷醇 Neo-menthol	9.97	0.12±0.01*	0.03±0.00	44	反式-橙花叔醇 Trans-nerolidol	15.28	0.41±0.21*	0.06±0.00
20	δ-松油醇 δ-terpineol	10.02	0.09±0.01	0.04±0.00	45	表荜澄茄油烯醇 Epicubenol	16.03	0.20±0.02*	0.08±0.01
21	4-萜品醇 L-terpinen-4-ol	10.17	4.46±0.76*	2.65±0.12	46	τ-杜松醇 τ-cadinol	16.31	2.36±0.04*	0.98±0.02
22	L-α-松油醇 L-α-terpineol	10.36	1.35±0.10*	0.68±0.02	47	吲哚-3-乙醛 Indole-3-acetaldehyde	16.96	0.08±0.03	-
23	4-烯丙基苯甲醚 Estragole	10.46	20.50±1.47*	13.9±2.26	48	新植二烯 Neophytadiene	18.29	0.69±0.10*	0.31±0.03
24	乙酸辛酯 Octyl ester acetic acid	10.57	0.32±0.04*	0.16±0.03	49	n-十六酸 n-hexadecanoic acid	19.46	0.18±0.01*	0.08±0.00
25	3-乙烯基-4-甲基-1H- 吡咯-2，5-二酮 3-ethenyl-4-methyl-1H-pyrrole-2，5-dione	11.25	0.17±0.01*	0.05±0.00	合计 Total amount/%			99.67	99.91

序号 No.	化合物名称 Compound name	保留时间 Retention time/min	含量 Content/%		序号 No.	化合物名称 Compound name	保留时间 Retention time/min	含量 Content/%
序号 No.	化合物名称 Compound name	保留时间 Retention time/min	CK	Cd	序号 No.	化合物名称 Compound name	保留时间 Retention time/min	CK	Cd
1	3-己烯醛 3-hexenal	4.13	1.86±0.16*	0.68±0.04	26	顺式-肉桂酸甲酯 Methyl cis-cinnamate	12.00	-	5.13±0.26
2	（E）-2-己烯醛（E）-2-hexenal	4.96	0.25±0.01*	0.08±0.00	27	丁香酚Eugenol	12.71	25.7±1.41*	0.02±0.01
3	顺式-3-己烯醇 Cis-3-hexenol	5.00	1.54±0.41*	0.14±0.04	28	肉桂酸甲酯 Methyl ester cinnamic acid	13.06	0.06±0.10	58.02±2.02*
4	α-侧柏烯 α-thujene	6.16	0.15±0.02*	0.06±0.01	29	β-榄香烯 β-elemene	13.21	0.83±0.09*	0.31±0.04
5	α-蒎烯 α-pinene	6.28	0.38±0.02*	0.21±0.01	30	甲基丁香酚 Methyl eugenol	13.28	6.56±0.14*	2.04±0.31
6	莰烯 Camphene	6.54	0.06±0.01	0.02±0.00	31	β-佛手柑油烯 β-bergamotene	13.49	0.10±0.01	0.05±0.01
7	香桧烯 Sabinene	6.93	0.14±0.01*	0.08±0.01	32	石竹烯 Caryophyllene	13.64	0.31±0.02*	0.16±0.01
8	β-蒎烯β-pinene	7.00	0.38±0.04*	0.19±0.01	33	反式-α-佛手柑油烯 Trans-α-bergamotene	13.76	2.41±0.11	2.09±0.05
9	β-月桂烯 β-myrcene	7.18	0.02±0.01	0.10±0.00*	34	顺式-β-金合欢烯Cis-β-farnesene	13.83	0.21±0.02	0.08±0.02
10	D-柠檬烯 D-limonene	7.83	0.32±0.00*	0.15±0.00	35	反式-β-金合欢烯 Trans-β-farnesene	13.95	0.29±0.03*	0.19±0.02
11	桉树脑 Eucalyptol	7.89	3.02±0.11*	1.95±0.09	36	蛇麻烯 Humulene	14.08	1.27±0.04*	0.70±0.02
12	（E）-β-罗勒烯（E）-β-ocimene	8.10	2.27±0.11*	1.13±0.02	37	顺式-4（15），5-依兰油二烯 Cis-muurola-4（15），5-diene	14.18	0.25±0.05*	0.08±0.01
13	γ-松油烯 γ-terpinene	8.30	0.40±0.02*	0.14±0.01	38	大根香叶烯 D Germacrene D	14.41	2.52±0.04*	1.18±0.02
14	顺式-水合香桧烯Cis-sabinene hydrate	8.46	0.79±0.05*	0.27±0.01	39	β-环大根香叶烷 β-cyclogermacrane	14.61	1.54±0.09*	0.4±0.01
15	萜品油烯 Terpinolene	8.78	0.14±0.01*	0.01±0.02	40	δ-愈创木烯 δ-guaiene	14.69	0.21±0.02*	0.06±0.02
16	葑酮 Fenchone	8.82	0.23±0.02	0.23±0.05	41	γ-杜松烯 γ-cadinene	14.80	1.07±0.04*	0.56±0.02
17	芳樟醇 Linalool	8.92	12.10±0.51*	4.15±0.19	42	β-倍半水芹烯 β-sesquiphellandrene	14.86	0.11±0.03	0.06±0.01
18	（+）-2-莰酮（+）-2-bornanone	9.71	0.85±0.03*	0.25±0.01	43	α-杜松烯 α-cadinene	15.01	0.09±0.02	0.03±0.00
19	新薄荷醇 Neo-menthol	9.97	0.12±0.01*	0.03±0.00	44	反式-橙花叔醇 Trans-nerolidol	15.28	0.41±0.21*	0.06±0.00
20	δ-松油醇 δ-terpineol	10.02	0.09±0.01	0.04±0.00	45	表荜澄茄油烯醇 Epicubenol	16.03	0.20±0.02*	0.08±0.01
21	4-萜品醇 L-terpinen-4-ol	10.17	4.46±0.76*	2.65±0.12	46	τ-杜松醇 τ-cadinol	16.31	2.36±0.04*	0.98±0.02
22	L-α-松油醇 L-α-terpineol	10.36	1.35±0.10*	0.68±0.02	47	吲哚-3-乙醛 Indole-3-acetaldehyde	16.96	0.08±0.03	-
23	4-烯丙基苯甲醚 Estragole	10.46	20.50±1.47*	13.9±2.26	48	新植二烯 Neophytadiene	18.29	0.69±0.10*	0.31±0.03
24	乙酸辛酯 Octyl ester acetic acid	10.57	0.32±0.04*	0.16±0.03	49	n-十六酸 n-hexadecanoic acid	19.46	0.18±0.01*	0.08±0.00
25	3-乙烯基-4-甲基-1H- 吡咯-2，5-二酮 3-ethenyl-4-methyl-1H-pyrrole-2，5-dione	11.25	0.17±0.01*	0.05±0.00	合计 Total amount/%			99.67	99.91

样品编号 Sample No.	Clean reads	GC含量 GC content/%	≥Q30/%	比对读数 Mapped reads	比对比率 Mapped ratio/%
0 h CK-1	22 830 057	49.84	93.02	17 200 093	75.34
0 h CK-2	22 391 222	49.80	92.93	17 070 648	76.24
0 h CK-3	21 181 042	50.05	93.88	16 240 183	76.67
24 h CK-1	21 485 915	50.28	93.29	16 070 383	74.79
24 hCK-2	21 898 153	50.27	93.37	16 540 511	75.53
24 h CK-3	21 872 539	50.81	93.37	16 650 456	76.12
72 h CK-1	22 127 839	49.96	93.08	16 819 392	76.01
72 h CK-2	20 937 711	50.20	93.83	15 897 564	75.93
72 h CK-3	19 962 929	50.29	93.46	15 148 810	75.88
24 h Cd-1	25 353 059	49.97	93.80	19 449 566	76.71
24 h Cd-2	20 283 780	49.74	93.89	15 626 179	77.04
24 h Cd-3	20 638 087	49.93	93.68	15 794 277	76.53
72 h Cd-1	20 774 226	49.12	93.32	15 927 385	76.67
72 h Cd-2	26 674 376	48.82	92.73	19 912 643	74.65
72 h Cd-3	22 262 126	48.62	93.14	16 647 781	74.78