Transcriptome Analysis of Potato Response to Pectobacterium atrosepticum Stress

doi:10.16420/j.issn.0513-353x.2025-0505

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (9): 2621-2638.doi: 10.16420/j.issn.0513-353x.2025-0505

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Transcriptome Analysis of Potato Response to Pectobacterium atrosepticum Stress

LUO Jinjun, HOU Lijuan, WANG Fei, MA Yongqiang^*()

Academy of Agriculture and Forestry Sciences，Qinghai University； Qinghai Key Laboratory of Agricultural Integrated Pest Management， Xining 810016， China

Received:2026-02-04 Revised:2026-05-20 Online:2026-09-25 Published:2026-09-20
Contact: MA Yongqiang

Abstract

Abstract:

Potato blackleg is one of the major diseases causing a decline in potato quality and yield，seriously threatening the healthy development of the potato industry. Pectobacterium atrosepticum was inoculated into plants of the resistant potato cultivar‘Longshu 19’，and RNA-Seq technology was used to explore the molecular mechanisms underlying the response of potato to Pectobacterium atrosepticum infection and to screen for key differentially expressed genes. The analysis results showed that compared with the control，436，20 411，and 3 759 differentially expressed genes（DEGs）were identified at 1，3，and 5 days post-inoculation，respectively，among which 77 were common DEGs. GO and KEGG enrichment analyses revealed that DEGs at 1 day post-inoculation were mainly enriched in lyase activity and secondary metabolite biosynthetic pathways；DEGs at 3 days were mainly enriched in catalytic activity and carbon metabolism pathways；and DEGs at 5 days were significantly associated with oxidoreductase activity and small molecule metabolic processes. Functional annotation of the 18 common DEGs enriched in metabolic pathways indicated that they encode defense-related proteins such as chitinase，peroxidase，and flavanone-3-hydroxylase. Screening for core pathways and core genes identified one core gene encoding flavanone-3-hydroxylase（Soltu.Q9. Chr02_A20006400.g，）and three transcription factors（belonging to the HD-ZIP and MYB families），among which StMYB1 may be a negative regulator of plant defense responses.

Key words: potato, blackleg disease, Pectobacterium atrosepticum, transcriptome analysis, differentially expressed gene

CLC Number:

S532马铃薯(土豆)

LUO Jinjun, HOU Lijuan, WANG Fei, MA Yongqiang. Transcriptome Analysis of Potato Response to Pectobacterium atrosepticum Stress[J]. Acta Horticulturae Sinica, 2026, 53(9): 2621-2638.

Figures/Tables 12

References 43

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样本 Sample	原始数据/bp Raw data	高质量数据/bp Clean data	Q20/%	Q30/%	GC/%	比对率/% Total_Mapped
L19CK1-1	6 362 609 400	5 781 020 989	98.04	94.21	44.35	28 660 578（68.23%）
L19CK1-2	5 985 569 100	5 176 874 626	98.09	94.34	44.65	25 534 224（64.99%）
L19CK1-3	5 899 996 800	5 313 762 764	98.17	94.56	44.47	26 099 598（67.04%）
L19CK3-1	5 700 715 200	4 833 788 241	97.85	93.83	44.49	25 392 182（67.75%）
L19CK3-2	5 548 576 200	4 613 056 168	98.19	94.60	44.33	24 838 280（68.30%）
L19CK3-3	6 191 647 500	5 148 648 984	98.16	94.54	44.36	28 053 153（69.00%）
L19CK5-1	6 545 884 800	5 745 110 894	97.95	94.02	44.54	27 673 060（64.35%）
L19CK5-2	5 589 375 600	4 935 724 332	98.24	94.64	44.72	22 530 668（61.25%）
L19CK5-3	5 968 323 000	5 073 046 832	97.98	94.17	44.48	25 407 721（64.86%）
L19T1-1	5 713 842 600	5 341 758 609	97.89	93.82	44.06	28 349 838（75.30%）
L19T1-2	6 517 583 100	6 001 113 996	97.97	94.02	44.47	29 399 065（68.40%）
L19T1-3	5 992 613 100	5 433 375 106	97.96	94.12	44.73	27 228 648（68.88%）
L19T3-1	5 475 185 700	4 637 734 971	98.03	94.24	43.23	29 926 633（83.59%）
L19T3-2	5 424 187 800	4 809 606 625	98.07	94.36	43.47	28 002 736（78.36%）
L19T3-3	6 399 372 600	5 477 611 586	97.96	94.12	44.18	29 220 089（69.63%）
L19T5-1	5 648 329 500	5 241 539 246	97.90	93.90	44.32	27 895 125（74.88%）
L19T5-2	5 990 732 100	5 374 183 518	98.00	94.21	43.89	30 612 243（77.60%）
L19T5-3	6 617 714 100	5 790 342 134	97.81	93.72	44.25	32 967 678（76.02%）
平均Mean	5 953 508 753	5 262 683 312	98.01	94.19	44.28	27 655 084（70.47%）

样本 Sample	原始数据/bp Raw data	高质量数据/bp Clean data	Q20/%	Q30/%	GC/%	比对率/% Total_Mapped
L19CK1-1	6 362 609 400	5 781 020 989	98.04	94.21	44.35	28 660 578（68.23%）
L19CK1-2	5 985 569 100	5 176 874 626	98.09	94.34	44.65	25 534 224（64.99%）
L19CK1-3	5 899 996 800	5 313 762 764	98.17	94.56	44.47	26 099 598（67.04%）
L19CK3-1	5 700 715 200	4 833 788 241	97.85	93.83	44.49	25 392 182（67.75%）
L19CK3-2	5 548 576 200	4 613 056 168	98.19	94.60	44.33	24 838 280（68.30%）
L19CK3-3	6 191 647 500	5 148 648 984	98.16	94.54	44.36	28 053 153（69.00%）
L19CK5-1	6 545 884 800	5 745 110 894	97.95	94.02	44.54	27 673 060（64.35%）
L19CK5-2	5 589 375 600	4 935 724 332	98.24	94.64	44.72	22 530 668（61.25%）
L19CK5-3	5 968 323 000	5 073 046 832	97.98	94.17	44.48	25 407 721（64.86%）
L19T1-1	5 713 842 600	5 341 758 609	97.89	93.82	44.06	28 349 838（75.30%）
L19T1-2	6 517 583 100	6 001 113 996	97.97	94.02	44.47	29 399 065（68.40%）
L19T1-3	5 992 613 100	5 433 375 106	97.96	94.12	44.73	27 228 648（68.88%）
L19T3-1	5 475 185 700	4 637 734 971	98.03	94.24	43.23	29 926 633（83.59%）
L19T3-2	5 424 187 800	4 809 606 625	98.07	94.36	43.47	28 002 736（78.36%）
L19T3-3	6 399 372 600	5 477 611 586	97.96	94.12	44.18	29 220 089（69.63%）
L19T5-1	5 648 329 500	5 241 539 246	97.90	93.90	44.32	27 895 125（74.88%）
L19T5-2	5 990 732 100	5 374 183 518	98.00	94.21	43.89	30 612 243（77.60%）
L19T5-3	6 617 714 100	5 790 342 134	97.81	93.72	44.25	32 967 678（76.02%）
平均Mean	5 953 508 753	5 262 683 312	98.01	94.19	44.28	27 655 084（70.47%）

基因ID Gene ID	名称 Name	拟南芥中同源基因ID The homologous gene ID in Arabidopsis was proposed	基因注释 Gene annotation	Pfam注释 Pfam_annotation
MSTRG.96421	CHI9	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr01_ A30000136.g	pod	ATCG00540.1	编码细胞色素f脱辅基蛋白 Encodes cytochrome f apoprotein	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr02_ A20006400.g	AN3	AT3G51240.2	编码黄烷酮-3-羟化酶 Encodes flavanone-3-hydroxylase	2-酮戊二酸依赖性氧化还原酶 2-Oxoglutarate-dependent oxidoreductases
Soltu.Q9.Chr02_ A20007278.g	9612	AT5G63180.1	果胶酸裂解酶 Pectate lyase	果胶裂解酶 Pectin lyase
Soltu.Q9.Chr02_ A30004811.g	CHI14	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr03_ A10009144.g	UPTG2	AT3G08900.1	可逆糖基化多肽Reversibly glycosylated polypeptide	核苷酸二磷酸糖转移酶 Nucleotide-diphospho-sugar transferases
Soltu.Q9.Chr04_ A30012653.g	EP3	AT3G54420.1	编码一种 EP3 几丁质酶 Encodes an EP3 chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr04_ A40012787.g	SHKA	AT1G22410.1	第二类DAHP 合成酶 DAHP synthetase class II	第二类DAHP合成酶、醛缩酶 I 类 DAHP synthetase class II，Aldolase class I
Soltu.Q9.Chr05_ A10014171.g	CHI3	AT5G05270.2	查尔酮—黄烷酮异构酶家族蛋白Chalcone-flavanone isomerase family protein	查尔酮—黄烷酮异构酶3样蛋白 Chalcone-flavonone isomerase 3-like
Soltu.Q9.Chr05_ A30014905.g	PNC1	AT5G05340.1	编码一种与过氧化物酶序列相似的蛋白质Encodes a protein with sequence similarity to peroxidases	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr05_ A40014836.g	PER3	AT1G05260.1	编码一种参与应激反应的冷诱导型阳离子过氧化物酶 Encodes a cold-inducible cationic peroxidase that is involved in the stress response	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr09_ A10021703.g	PRP1	AT2G29420.1	编码属于GST的tau类谷胱甘肽转移酶Encodes glutathione transferase belonging to the tau class of GSTs	谷胱甘肽S-转移酶 Omega/Tau样 Glutathione S-transferase Omega/Tau-like
Soltu.Q9.Chr09_ A20024039.g	CHS1B	AT5G13930.1	编码查尔酮合酶 Encodes chalcone synthase	III 型聚酮合酶 Polyketide synthase，type III
Soltu.Q9.Chr10_ A10025644.g	PER21	AT2G37130.2	过氧化物酶超家族蛋白 Peroxidase superfamily protein	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr10_ A30027390.g	PDC4	AT5G54960.1	丙酮酸脱羧酶 Pyruvate decarboxylase	丙酮酸脱羧酶/吲哚丙酮酸脱羧酶样 Pyruvate decarboxylase/indolepyruvate decarboxylase-like
Soltu.Q9.Chr10_ A40026571.g	TD1	AT3G10050.1	异亮氨酸生物合成途径中的催化酶Catalytic enzyme in the isoleucine biosynthetic pathway	丝氨酸/苏氨酸脱水酶 Serine/Threonine dehydratase
Soltu.Q9.Chr12_ A10028456.g	LAP	ATMG00960.1	编码线粒体膜的一种蛋白质 Encodes a protein of the mitochondrial membrane	肽酶 M17、亮氨酸氨肽酶/肽酶 B Peptidase M17，Leucine aminopeptidase/ Peptidase B
Soltu.Q9.contigutg00 0299l_4193999_4342 8920000164.g	CHTB3	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase

基因ID Gene ID	名称 Name	拟南芥中同源基因ID The homologous gene ID in Arabidopsis was proposed	基因注释 Gene annotation	Pfam注释 Pfam_annotation
MSTRG.96421	CHI9	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr01_ A30000136.g	pod	ATCG00540.1	编码细胞色素f脱辅基蛋白 Encodes cytochrome f apoprotein	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr02_ A20006400.g	AN3	AT3G51240.2	编码黄烷酮-3-羟化酶 Encodes flavanone-3-hydroxylase	2-酮戊二酸依赖性氧化还原酶 2-Oxoglutarate-dependent oxidoreductases
Soltu.Q9.Chr02_ A20007278.g	9612	AT5G63180.1	果胶酸裂解酶 Pectate lyase	果胶裂解酶 Pectin lyase
Soltu.Q9.Chr02_ A30004811.g	CHI14	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr03_ A10009144.g	UPTG2	AT3G08900.1	可逆糖基化多肽Reversibly glycosylated polypeptide	核苷酸二磷酸糖转移酶 Nucleotide-diphospho-sugar transferases
Soltu.Q9.Chr04_ A30012653.g	EP3	AT3G54420.1	编码一种 EP3 几丁质酶 Encodes an EP3 chitinase	糖苷水解酶 Glycoside hydrolase
Soltu.Q9.Chr04_ A40012787.g	SHKA	AT1G22410.1	第二类DAHP 合成酶 DAHP synthetase class II	第二类DAHP合成酶、醛缩酶 I 类 DAHP synthetase class II，Aldolase class I
Soltu.Q9.Chr05_ A10014171.g	CHI3	AT5G05270.2	查尔酮—黄烷酮异构酶家族蛋白Chalcone-flavanone isomerase family protein	查尔酮—黄烷酮异构酶3样蛋白 Chalcone-flavonone isomerase 3-like
Soltu.Q9.Chr05_ A30014905.g	PNC1	AT5G05340.1	编码一种与过氧化物酶序列相似的蛋白质Encodes a protein with sequence similarity to peroxidases	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr05_ A40014836.g	PER3	AT1G05260.1	编码一种参与应激反应的冷诱导型阳离子过氧化物酶 Encodes a cold-inducible cationic peroxidase that is involved in the stress response	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr09_ A10021703.g	PRP1	AT2G29420.1	编码属于GST的tau类谷胱甘肽转移酶Encodes glutathione transferase belonging to the tau class of GSTs	谷胱甘肽S-转移酶 Omega/Tau样 Glutathione S-transferase Omega/Tau-like
Soltu.Q9.Chr09_ A20024039.g	CHS1B	AT5G13930.1	编码查尔酮合酶 Encodes chalcone synthase	III 型聚酮合酶 Polyketide synthase，type III
Soltu.Q9.Chr10_ A10025644.g	PER21	AT2G37130.2	过氧化物酶超家族蛋白 Peroxidase superfamily protein	血红素过氧化物酶 Heme-peroxidase
Soltu.Q9.Chr10_ A30027390.g	PDC4	AT5G54960.1	丙酮酸脱羧酶 Pyruvate decarboxylase	丙酮酸脱羧酶/吲哚丙酮酸脱羧酶样 Pyruvate decarboxylase/indolepyruvate decarboxylase-like
Soltu.Q9.Chr10_ A40026571.g	TD1	AT3G10050.1	异亮氨酸生物合成途径中的催化酶Catalytic enzyme in the isoleucine biosynthetic pathway	丝氨酸/苏氨酸脱水酶 Serine/Threonine dehydratase
Soltu.Q9.Chr12_ A10028456.g	LAP	ATMG00960.1	编码线粒体膜的一种蛋白质 Encodes a protein of the mitochondrial membrane	肽酶 M17、亮氨酸氨肽酶/肽酶 B Peptidase M17，Leucine aminopeptidase/ Peptidase B
Soltu.Q9.contigutg00 0299l_4193999_4342 8920000164.g	CHTB3	AT3G12500.1	编码一种碱性几丁质酶 Encodes a basic chitinase	糖苷水解酶 Glycoside hydrolase

TF家族 TF family	名称 Name	基因ID Gene ID	L19CK1-vs.-L19T1	L19CK3-vs.-L19T3	L19CK5-vs.-L19T5
HD-ZIP	HAT4	Soltu.Q9.Chr08_A20021612.g	上调 Up	下调 Down	下调 Down
HD-ZIP	HAT4	Soltu.Q9.Chr08_A40022004.g	上调 Up	下调 Down	下调 Down
MYB	MYB1	Soltu.Q9.Chr10_A40026227.g	下调 Down	下调 Down	下调 Down

Transcriptome Analysis of Potato Response to Pectobacterium atrosepticum Stress

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基因ID Gene ID	时期（核心通路） Period（Core pathway）	名称 Name	基因注释 Gene annotation
Soltu.Q9.Chr02_A20006400.g*	L19CK1-vs.-L19T1（ko01100）	AN3	编码黄烷酮-3-羟化酶 Encodes flavanone-3-hydroxylase
Soltu.Q9.Chr05_A20013308.g	L19CK1-vs.-L19T1（ko01100）	AMY3	果胶酸裂解酶 Pectate lyase
Soltu.Q9.Chr04_A20010379.g	L19CK3-vs.-L19T3（ko00620）	E1-BETA-2	丙酮酸脱氢酶 Pyruvate dehydrogenase
Soltu.Q9.Chr04_A20010396.g		E1-BETA-2	丙酮酸脱氢酶 Pyruvate dehydrogenase
Soltu.Q9.Chr05_A20013367.g		Os02g0739600	丙酮酸脱氢酶 Pyruvate dehydrogenase
Soltu.Q9.Chr05_A30013581.g		Os02g0739600	丙酮酸脱氢酶 Pyruvate dehydrogenase
Soltu.Q9.Chr06_A30018221.g		Os08g0536000	转酮醇酶家族蛋白 Transketolase family protein
Soltu.Q9.Chr08_A30021838.g		E1-BETA-2	丙酮酸脱氢酶 Pyruvate dehydrogenase
Soltu.Q9.Chr08_A20019142.g	L19CK5-vs.-L19T5（ko01100）	HMGS	编码羟甲基戊二酰辅酶A合酶样蛋白Encodes hydroxymethylglutaryl-CoA synthase-like
Soltu.Q9.Chr08_A20019166.g		HMGS	编码羟甲基戊二酰辅酶A合酶样蛋白Encodes hydroxymethylglutaryl-CoA synthase-like
Soltu.Q9.Chr08_A40020209.g		HMGS	编码羟甲基戊二酰辅酶A合酶样蛋白Encodes hydroxymethylglutaryl-CoA synthase-like
Soltu.Q9.Chr12_A20030203.g		HMGS	编码羟甲基戊二酰辅酶A合酶样蛋白Encodes hydroxymethylglutaryl-CoA synthase-like

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