Comparative Transcriptome Analysis of Differential Expression in Different Tissues of Corydalis yanhusuo

doi:10.16420/j.issn.0513-353x.2021-0822

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (1): 177-187.doi: 10.16420/j.issn.0513-353x.2021-0822

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Comparative Transcriptome Analysis of Differential Expression in Different Tissues of Corydalis yanhusuo

ZHAO Xueyan¹, WANG Qi², WANG Li¹, WANG Fangyuan¹, WANG Qing¹, LI Yan¹^,^*()

¹Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources，Xi’an Botanical Garden of Shaanxi Province，Institute of Botany of Shaanxi Province，Xi’an 710061，China
²School of Pharmacy，Shaanxi Institute of International Trade and Commerce，Xianyang，Shaanxi 712046，China

Received:2021-11-08 Revised:2022-06-03 Online:2023-01-25 Published:2023-01-18
Contact: *（E-mail：5214352@126.com）

Abstract

Abstract:

The dried tubers of Corydalis yanhusuo can be used as the traditional Chinese medicine，and isoquinoline alkaloid compounds are the main active ingredient. To identify genes related to isoquinoline alkaloid biosynthesis and analyze the differentially expressed genes of tuber，rhizome and leaf tissues of C. yanhusuo，transcriptome sequencing of these tissues using Illumina high-throughput sequencing technology were performed. A total of 6 161，8 852 and 5 772 differentially expressed genes were identified in comparisons of tuber vs. rhizome，tuber vs. leaf and rhizome vs. leaf，respectively．KEGG enrichment analysis of differentially expressed genes indicated that major enrichment pathways were starch and sucrose metabolism，phenylpropanine biosynthesis，plant hormone signal transduction and isoquinoline alkaloid biosynthesis pathways. Fourty-seven transcripts were identified to be related to isoquinoline alkaloid biosynthesis and the highest level of gene expression was found in tuber，following by rhizome and leaf.

Key words: Corydalis yanhusuo, isoquinoline alkaloids, transcriptome, expression analysis

CLC Number:

S567

ZHAO Xueyan, WANG Qi, WANG Li, WANG Fangyuan, WANG Qing, LI Yan. Comparative Transcriptome Analysis of Differential Expression in Different Tissues of Corydalis yanhusuo [J]. Acta Horticulturae Sinica, 2023, 50(1): 177-187.

Figures/Tables 8

References 32

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基因名称（编号） Gene name（ID）	正向引物序列（5′-3′） Forward primer sequence	反向引物序列（5′-3′） Reverse primer sequence
Actin (AT1G49240)	GGTAACATTGTGCTCAGTGGTGG	AACGACCTTAATCTTCATGCTGC
NCS（transcript_36281）	TAGCAAGCATGGCAGCAGTCATC	TAGCCACCTCCACCTCTGTTGTC
6OMT（transcript_4831）	AGGGACTGGTCACTTGGGATCG	AAAAGGCGTCGGTGCATCGG
CNMT（transcript_29289）	AGTGGGAAGCATTTCTCACGTACC	TTCCTCCATGATTGCCATCACTGC
NMCH（transcript_4028）	GCCAAAGCCCAATCAAGGAATCAG	TGGGGTTGGAGGGTGAAGTCTTAG
4’OMT（transcript_4823）	CGTAGCACTGGAGGAGGGATCTG	CCTTTCTCTCCCACCTGTGTTCAC
SOMT（transcript_19389）	TTGCTGGGAAGGAGCCAAAAGTG	ACCACCACCAACATCAACCAACTC

基因名称（编号） Gene name（ID）	正向引物序列（5′-3′） Forward primer sequence	反向引物序列（5′-3′） Reverse primer sequence
Actin (AT1G49240)	GGTAACATTGTGCTCAGTGGTGG	AACGACCTTAATCTTCATGCTGC
NCS（transcript_36281）	TAGCAAGCATGGCAGCAGTCATC	TAGCCACCTCCACCTCTGTTGTC
6OMT（transcript_4831）	AGGGACTGGTCACTTGGGATCG	AAAAGGCGTCGGTGCATCGG
CNMT（transcript_29289）	AGTGGGAAGCATTTCTCACGTACC	TTCCTCCATGATTGCCATCACTGC
NMCH（transcript_4028）	GCCAAAGCCCAATCAAGGAATCAG	TGGGGTTGGAGGGTGAAGTCTTAG
4’OMT（transcript_4823）	CGTAGCACTGGAGGAGGGATCTG	CCTTTCTCTCCCACCTGTGTTCAC
SOMT（transcript_19389）	TTGCTGGGAAGGAGCCAAAAGTG	ACCACCACCAACATCAACCAACTC

样品 Sample	Clean read 数量 Clean read number	碱基数 Base number	GC/%	% ≥ Q30	比对率/% Mapped ratio
块茎 Tuber	20 214 211	6 055 395 267	43.43	93.21	86.72
根茎 Rhizome	21 439 743	6 422 326 271	43.24	93.17	72.78
叶 Leaf	24 116 972	7 222 883 792	43.40	93.40	71.96

样品 Sample	Clean read 数量 Clean read number	碱基数 Base number	GC/%	% ≥ Q30	比对率/% Mapped ratio
块茎 Tuber	20 214 211	6 055 395 267	43.43	93.21	86.72
根茎 Rhizome	21 439 743	6 422 326 271	43.24	93.17	72.78
叶 Leaf	24 116 972	7 222 883 792	43.40	93.40	71.96

样品对比 Sample pair	总数 All	COG	GO	KEGG	KOG	Pfam	Swiss-Prot	eggNOG	Nr
块茎 vs. 根茎 Tuber vs. Rhizome	5 869	2 735	4 201	2 420	3 341	4 995	4.667	5 723	5 846
块茎 vs. 叶 Tuber vs. Leaf	8 487	3 989	6 126	3 937	5 234	7 270	6.629	8 261	8 458
根茎 vs. 叶 Rhizome vs. Leaf	5 529	2 674	3 989	2 557	3 465	4 741	4.340	5 361	5 508

Comparative Transcriptome Analysis of Differential Expression in Different Tissues of Corydalis yanhusuo

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块茎 vs. 根茎 Tuber vs. Rhizome			块茎 vs. 叶 Tuber vs. Leaf			根茎 vs. 叶 Rhizome vs. Leaf
注释 Annotation	数量 Number	Ks	注释 Annotation	数量 Number	Ks	注释 Annotation	数量 Number	Ks
多糖分解 Polysaccharide catabolic	242	1.0E-30	翻译 Translation	521	4.7E-25	氧化还原 Oxidation-reduction	481	2.3E-17
淀粉生物合成 Starch biosynthetic	29	6.2E-10	多糖分解Polysaccharide catabolic	240	1.1E-19	翻译Translation	365	4.9E-14
糖原生物合成Glycogen biosynthetic	24	8.9E-8	细胞质翻译Cytoplasmic translation	39	2.1E-9	核糖体小亚基组装Ribosomal small subunit assembly	24	2.3E-6
亚精胺生物合成Spermidine biosynthetic	11	4.9E-7	核糖体小亚基组装Ribosomal small subunit assembly	28	4.3E-9	次生代谢产物合成Secondary metabolite biosynthetic	41	9.5E-6
异喹啉生物碱生物合成Isoquinoline alkaloid biosynthetic	24	5.3E-7	次生代谢产物合成Secondary metabolite biosynthetic	54	8.1E-7	谷胱甘肽代谢Glutathione metabolic	18	1.9E-5
蛋白磷酸化 Protein phosphorylation	290	7.2E-7	氧化还原 Oxidation-reduction	634	2.0E-6	寡肽运输 Oligopeptide transport	11	4.0E-5
次生代谢产物合成Secondary metabolite biosynthetic	44	9.3E-7	氨基酸跨膜转运 Amino acid transmembrane transport	24	3.7E-6	芥子油苷分解Glucosinolate catabolic	8	0.00012
药物跨膜运输Drug transmembrane transport	26	9.3E-7	亚精胺生物合成Spermidine biosynthetic	11	1.8E-5	（S）-心果碱代谢（S）-reticuline metabolic	10	0.00014
淀粉分解 Starch catabolic	25	7.3E-6	精氨酸分解 Arginine catabolic	8	2.5E-5	细胞质翻译 Cytoplasmic translation	28	0.00014
块茎 vs. 根茎 Tuber vs. Rhizome			块茎 vs. 叶 Tuber vs. Leaf			根茎 vs. 叶 Rhizome vs. Leaf
注释 Annotation	数量 Number	Ks	注释 Annotation	数量 Number	Ks	注释 Annotation	数量 Number	Ks
（S）-心果碱代谢（S）-reticuline metabolic	17	1.4E-5	对真菌的响应 Response to molecule of fungal origin	21	3.8E-5	L-苯丙氨酸分解 L-phenylalanine catabolic	8	0.00015
膜整体部分 Integral component of membrane	1 116	1.2E-12	胞质大核糖体亚基Cytosolic large ribosomal subunit	146	7.6E-26	胞质小核糖体亚基Cytosolic small ribosomal subunit	78	3.2E-17
细胞壁 Cell wall	125	3.4E-9	胞质小核糖体亚基Cytosolic small ribosomal subunit	88	6.3E-24	胞质大核糖体亚基Cytosolic large ribosomal subunit	104	1.4E-15
胞外区 Extracellular region	129	4.5E-9	核糖体 Ribosome	398	1.6E-11	核糖体 Ribosome	297	3.7E-8
质膜部分 Integral component of plasma membrane	63	3.7E-8	叶绿体 Chloroplast	536	1.1E-10	叶绿体基质 Chloroplast stroma	126	5.2E-8
β-淀粉酶活性 Beta-amylase activity	180	1.0E-30	核糖体结构Structural constituent of ribosome	379	1.0E-30	核糖体结构 Structural constituent of ribosome	289	1.0E-30
水解酶活性 Hydrolase activity，hydrolyzing O-glycosyl compounds	338	6.5E-9	β-淀粉酶活性 β-amylase activity	179	6.3E-23	铁离子结合Iron ion binding	81	1.2E-8
药物跨膜运输 Drug transmembrane transporter	26	1.1E-6	rRNA结合 rRNA binding	81	1.6E-12	血红素结合 Heme binding	81	4.8E-8
催化活性 Catalytic activity	2 450	1.9E-6	大核糖体亚基rRNA结合 Large ribosomal subunit rRNA binding	16	6.9E-7	单加氧酶活性Monooxygenase activity	82	2.0E-7
葡萄糖-1-磷酸-腺苷转移酶活性Glucose-1-phosphate adenylyltransferase activity	11	2.6E-6	氨基酸跨膜运输活性 Amino acid transmembrane transporter activity	26	5.2E-6	rRNA结合 rRNA binding	57	4.1E-6
半胱氨酸肽链内切酶 Cysteine-type endopeptidase activity	19	2.9E-6	氧化还原酶活性Oxidoreductase activity	55	6.1E-6	过氧化物酶活性 Peroxidase activity	40	3.6E-5
氧化还原酶活性Oxidoreductase activity	47	6.2E-6	2-链烯还原酶活性 2-Alkenal reductase [NAD（P）]activity	54	3.0E-5	氧化还原酶活性Oxidoreductase activity	82	4.9E-5
精氨酸脱羧酶活性 Arginine decarboxylase activity	6	2.2E-5	磷酸转移激酶活性 Phosphorelay sensor kinase activity	14	4.7E-5	β-葡糖苷酶活性β-glucosidase activity	22	6.0E-5

块茎 vs. 根茎 Tuber vs. Rhizome			块茎 vs. 叶 Tuber vs. Leaf			根茎 vs. 叶 Rhizome vs. Leaf
代谢通路 Pathway	数量 Number	P	代谢通路 Pathway	数量Number	P	代谢通路 Pathway	数量Number	P
淀粉和蔗糖代谢 Starch and sucrose metabolism	152	1.0E-19	核糖体 Ribosome	379	2.9E-61	核糖体 Ribosome	291	8.67E-46
植物激素信号转导 Plant hormone signal transduction	85	1.8E-6	淀粉和蔗糖代谢 Starch and sucrose metabolism	179	6.9E-8	苯丙素生物合成Phenylpropanoid biosynthesis	70	1.83E-08
半乳糖代谢 Galactose metabolism	44	2.7E-6	苯丙素生物合成Phenylpropanoid biosynthesis	76	0.0012	氰基氨基酸代谢Cyanoamino acid metabolism	39	5.13E-06
块茎 vs. 根茎 Tuber vs. Rhizome			块茎 vs. 叶 Tuber vs. Leaf			根茎 vs. 叶 Rhizome vs. Leaf
代谢通路 Pathway	数量 Number	P	代谢通路 Pathway	数量Number	P	代谢通路 Pathway	数量Number	P
植物与病原菌互作 Plant-pathogen interaction	67	4.0E-5	植物激素信号转导 Plant hormone signal transduction	109	0.0071	光合作用有机体碳固定 Carbon fixation in photosynthetic organisms	51	0.0147
苯丙素生物合成 Phenylpropanoid biosynthesis	59	7.1E-6	氰基氨基酸代谢Cyanoamino acid metabolism	42	0.0054	生理节律—植物 Circadian rhythm - plant	29	0.0041
亚油酸代谢 Linoleic acid metabolism	16	0.0001	亚油酸代谢 Linoleic acid metabolism	17	0.0254	谷胱甘肽代谢 Glutathione metabolism	41	0.0236
醚脂类代谢 Ether lipid metabolism	19	0.0202	α-亚麻酸代谢α-Linolenic acid metabolism	34	0.0682	半胱氨酸和蛋氨酸代谢 Cysteine and methionine metabolism	63	0.0364
异喹啉生物碱生物合成Isoquinoline alkaloid biosynthesis	26	0.0674	乙醛酸和二羧酸的代谢Glyoxylate and dicarboxylate metabolism	58	0.1629	苯丙氨酸，酪氨酸和色氨酸合成Phenylalanine，tyrosine and tryptophan biosynthesis	33	0.0974
核糖体 Ribosome	156	0.0919	光合作用有机体碳固定Carbon fixation in photosynthetic organisms	61	0.4460	淀粉和蔗糖代谢 Starch and sucrose metabolism	114	0.1132
氨基糖和核苷酸糖的代谢 Amino sugar and nucleotide sugar metabolism	54	0.0997	生理节律-植物 Circadian rhythm-plant	31	0.6627	抗坏血酸和醛糖酸代谢Ascorbate and aldarate metabolism	28	0.1157
α-亚麻酸代谢 α-Linolenic acid metabolism	24	0.1153	抗坏血酸和醛糖酸代谢Ascorbate and aldarate metabolism	31	1.0000	异喹啉生物碱生物合成Isoquinoline alkaloid biosynthesis	28	0.1157
丙氨酸、天冬氨酸、谷氨酸代谢Alanine，aspartate and glutamate metabolism	34	0.4667	氨基酸生物合成Biosynthesis of amino acids	190	1.0000	酪氨酸代谢 Tyrosine metabolism	31	0.2676
ABC转运体 ABC transporters	14	0.5534	类胡萝卜素生物合成Carotenoid biosynthesis	18	1.0000	甘油脂类代谢 Glycerolipid metabolism	36	0.4619
精氨酸和脯氨酸代谢 Arginine and proline metabolism	23	0.7312	果糖和甘露糖代谢 Fructose and mannose metabolism	36	1.0000	油菜素内脂生物合成Brassinosteroid biosynthesis	13	0.6647
戊糖、葡萄糖醛酸转换 Pentose and glucuronate interconversions	23	0.7312	糖酵解/糖异生Glycolysis/ Gluconeogenesis	90	1.0000	卟啉和叶绿素代谢Porphyrin and chlorophyll metabolism	23	0.8207
氮代谢 Nitrogen metabolism	12	0.9688	氮代谢 Nitrogen metabolism	15	1.0000	丙氨酸、天冬氨酸、谷氨酸代谢 Alanine，aspartate and glutamate metabolism	35	1.0000
花生四烯酸代谢 Arachidonic acid metabolism	7	1.0000	戊糖、葡萄糖醛酸转换Pentose and glucuronate interconversions	32	1.0000	戊糖、葡萄糖醛酸转换Pentose and glucuronate interconversions	24	1.0000
半胱氨酸和蛋氨酸代谢 Cysteine and methionine metabolism	50	1.0000	磷酸戊糖途径Pentose phosphate pathway	46	1.0000	有机含硒化合物代谢Selenocompound metabolism	20	1.0000
类固醇生物合成 Steroid biosynthesis	20	1.0000	类固醇生物合成 Steroid biosynthesis	28	1.0000	类固醇生物合成 Steroid biosynthesis	22	1.0000
维生素B6代谢 Vitamin B6 metabolism	7	1.0000	缬氨酸、亮氨酸和异亮氨酸的降解 Valine，leucine and isoleucine degradation	41	1.00000	芪类、二芳基庚烷和姜酚生物合成 Stilbenoid，diarylheptanoid and gingerol biosynthesis	9	1.0000

简称 Abbreviation	全称 Full name	基因编号 Gene ID
NCS	(S)-去甲基乌药碱合酶 (S)-norcoclaurine synthase	transcript_17057，transcript_19226，transcript_543，transcript_5764，transcript_34030，transcript_13099，transcript_21615，transcript_9018，transcript_5209，transcript_36281，transcript_527，transcript_8823
6OMT	(S)-去甲基乌药碱-6-氧甲基转移酶 (S)-norcoclaurine 6-O-methyltransferase	transcript_33869，transcript_4831，transcript_19521，transcript_21316，transcript_26993，transcript_21935，transcript_27053，transcript_32190，transcript_4822，transcript_4816，transcript_31617，transcript_6804，transcript_4484，transcript_32370，transcript_22232，transcript_4266
CNMT	(S)-乌药碱-N-甲基转移酶 (S)-coclaurine-N-methyltransferase	transcript_29289，transcript_16285，transcript_15928，transcript_21025，transcript_24962，transcript_4897，transcript_23886，transcript_20924，transcript_3652
NMCH	(S)-羟基-N-甲基乌药碱羟化酶 (S)-N-methylcoclaurine hydroxylase	transcript_33528，transcript_4028
4’OMT	(S)-羟基-N-甲基乌药碱-4’-O-甲基转移酶 (S)-3’-hydroxy-N-methylcoclaurine-4’-O-methyltransferase	transcript_4823，transcript_33789
SOMT	(S)-金黄紫堇碱-9-O-甲基转移酶 (S)-scoulerine-9-O-methyltransferasese	transcript_19389，transcript_27465，transcript_5219，transcript_26864，transcript_8610，transcript_4164

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