Analysis of Response Mechanism of Ligusticum chuanxiong to Cadmium Stress Based on Transcriptome and Metabolome

doi:10.13304/j.nykjdb.2024.0022

Abstract

Abstract:

In order to understand the changes of gene expression and metabolites of Ligusticum chuanxiong under different levels of cadmium （Cd） stress， and explore the response mechanism of Ligusticum Chuanxiong to Cd stress， a pot experiment was conducted， and 4 Cd stress treatment levels of 1， 3， 6， 9 mg·kg^-1 were set with clean soil without adding Cd solution as control group，and RNA sequencing（RNA-seq） and ultra performance liquid chromatography tandem mass spectrometry （UPLC-MS/MS） were used to identify key genes and metabolic pathways for resistance to Cd stress in Ligusticum chuanxiong. The results showed that a total of 8 569 differentially expressed genes were screened， including 6 859 up-regulated genes and 1 710 down-regulated genes. Compared with the control group， there was only 1 common differential gene in the 4 Cd-treated groups， CML19， which might be the key gene for resistance to Cd stress in Ligusticum chuanxiong. The metabolome labeled and quantized 1 238 different metabolites， and 76 metabolic pathways were annotated in the KEGG database， including amino acid metabolism， biosynthesis of aminoacyl-tRNA and biosynthesis of fatty acids. The joint analysis showed that Ligusticum chuanxiong played an important role in the resistance to Cd stress by regulating different amino acids to maintain its own metabolic balance when subjected to different levels of Cd stress. Above results provided scientific support and theoretical basis for the resistance of Ligusticum chuanxiong to Cd stress， and provided a basis for the subsequent cultivation and breeding of Ligusticum chuanxiong resources and related research on alleviating Cd stress.

Key words: Ligusticum chuanxiong, cadmium stress, transcriptome, metabolome

摘要：

为了解不同水平镉（Cd）胁迫下川芎基因表达和代谢产物的变化规律，探究川芎对Cd胁迫的响应机制，利用盆栽试验，以不添加Cd溶液的清洁土壤为对照，设置1、3、6、10 mg·kg^-1共4个Cd胁迫处理水平，采用转录组学测序（RNA sequencing，RNA-seq）和超高效液相色谱质谱联用（ultra performance liquid chromatography tandem mass spectrometry，UPLC-MS/MS）技术，筛选川芎抗Cd胁迫的关键基因与代谢通路。结果表明，共筛选到8 569个差异表达基因，包括上调基因6 859个，下调基因1 710个。与对照相比，4个Cd处理组的共有差异基因仅1个，为CML19，可能是川芎抗Cd胁迫的关键基因。代谢组共标注和定量了1 238种差异代谢物，在KEGG数据库中注释得到76条代谢通路，其中包括氨基酸代谢、氨酰基-tRNA的生物合成和脂肪酸的生物合成等。联合分析表明，当受到不同水平Cd胁迫时，川芎通过调节不同种类氨基酸来维持自身代谢平衡，在川芎抗Cd胁迫中发挥重要作用。研究结果为川芎抗Cd胁迫提供科学支撑与理论依据，为针对川芎资源的栽培育种及缓解Cd胁迫等相关研究提供基础。

关键词: 川芎, 镉胁迫, 转录组, 代谢组

CLC Number:

S567.21

Wanjing XU, Fang PENG, Doudou ZHAO, Jiaojiao LUO, Shan TAO, Hailang LIAO, Changqing MAO, Yu WU, Xiu ZHU, Zhengjun XU, Chao ZHANG. Analysis of Response Mechanism of Ligusticum chuanxiong to Cadmium Stress Based on Transcriptome and Metabolome[J]. Journal of Agricultural Science and Technology, 2024, 26(10): 98-109.

徐皖菁, 彭芳, 赵豆豆, 罗姣姣, 陶珊, 廖海浪, 毛常清, 吴宇, 朱秀, 徐正君, 张超. 基于转录组和代谢组解析川芎对镉胁迫的响应机制[J]. 中国农业科技导报, 2024, 26(10): 98-109.

Figures/Tables 8

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样品编号 Sample number	Clean reads数目 Number of clean reads	总碱基数 Total base number/nt	GC含量 GC content/%	Q30/%
CK-1	29 678 610	8 835 337 288	43.62	93.76
CK-2	24 429 573	7 276 365 402	43.79	93.26
CK-3	19 868 507	5 905 914 150	44.19	93.33
Cd1-1	20 935 573	6 215 766 952	44.79	93.93
Cd1-2	25 071 449	7 465 487 210	43.97	93.66
Cd1-3	21 681 836	6 460 887 440	43.92	93.61
Cd3-1	19 483 124	5 787 607 824	43.61	93.79
Cd3-2	20 832 819	6 215 838 452	43.87	93.05
Cd3-3	21 394 788	6 382 109 148	43.90	93.59
Cd6-1	20 610 107	6 120 785 704	43.97	93.70
Cd6-2	20 640 197	6 157 201 056	43.79	93.78
Cd6-3	22 624 009	6 720 661 646	43.88	93.87
Cd10-1	19 376 308	5 766 904 348	43.94	93.65
Cd10-2	19 731 742	5 880 325 626	43.67	93.46
Cd10-3	21 006 650	6 270 393 312	43.95	93.36
合计 Total	327 365 292	97 461 585 558	—	—

样品编号 Sample number	Clean reads数目 Number of clean reads	总碱基数 Total base number/nt	GC含量 GC content/%	Q30/%
CK-1	29 678 610	8 835 337 288	43.62	93.76
CK-2	24 429 573	7 276 365 402	43.79	93.26
CK-3	19 868 507	5 905 914 150	44.19	93.33
Cd1-1	20 935 573	6 215 766 952	44.79	93.93
Cd1-2	25 071 449	7 465 487 210	43.97	93.66
Cd1-3	21 681 836	6 460 887 440	43.92	93.61
Cd3-1	19 483 124	5 787 607 824	43.61	93.79
Cd3-2	20 832 819	6 215 838 452	43.87	93.05
Cd3-3	21 394 788	6 382 109 148	43.90	93.59
Cd6-1	20 610 107	6 120 785 704	43.97	93.70
Cd6-2	20 640 197	6 157 201 056	43.79	93.78
Cd6-3	22 624 009	6 720 661 646	43.88	93.87
Cd10-1	19 376 308	5 766 904 348	43.94	93.65
Cd10-2	19 731 742	5 880 325 626	43.67	93.46
Cd10-3	21 006 650	6 270 393 312	43.95	93.36
合计 Total	327 365 292	97 461 585 558	—	—

数据库 Database	Unigenes数量 Number of unigenes
数据库 Database	总量 Total	300≤长度<1 000 bp 300≤Length<1 000 bp	长度≥1 000 bp Length≥1 000 bp	占比 Proportion/%
COG	11 717	4 635	7 082	32.25
GO	28 277	11 510	16 747	77.82
KEGG	23 357	9 252	14 105	64.28
KOG	21 487	8 946	12 541	59.13
Pfam	28 001	10 941	17 060	77.06
Swiss-Prot	22 042	8 924	13 118	60.66
TrEMBL	31 952	13 037	18 915	87.93
EggNOG4.5	26 245	10 422	15 823	72.23
NR	34 643	14 628	20 015	95.34
总注释转录本 Total annotated transcript	36 336	15 887	20 429	100.00

数据库 Database	Unigenes数量 Number of unigenes
数据库 Database	总量 Total	300≤长度<1 000 bp 300≤Length<1 000 bp	长度≥1 000 bp Length≥1 000 bp	占比 Proportion/%
COG	11 717	4 635	7 082	32.25
GO	28 277	11 510	16 747	77.82
KEGG	23 357	9 252	14 105	64.28
KOG	21 487	8 946	12 541	59.13
Pfam	28 001	10 941	17 060	77.06
Swiss-Prot	22 042	8 924	13 118	60.66
TrEMBL	31 952	13 037	18 915	87.93
EggNOG4.5	26 245	10 422	15 823	72.23
NR	34 643	14 628	20 015	95.34
总注释转录本 Total annotated transcript	36 336	15 887	20 429	100.00

分组 Group	差异表达基因总数 Total number of differentially expressed genes	上调 Up	下调 Down
CK vs Cd1	2 385	2 247	138
CK vs Cd3	5 703	4 205	1 498
CK vs Cd6	286	257	29
CK vs Cd10	195	150	45
合计 Total	8 569	6 859	1 710