核桃黑斑病生防链霉菌WMF106全基因组测序及分析

doi:10.11924/j.issn.1000-6850.casb2026-0011

中国农学通报 ›› 2026, Vol. 42 ›› Issue (12): 144-154.doi: 10.11924/j.issn.1000-6850.casb2026-0011

核桃黑斑病生防链霉菌WMF106全基因组测序及分析

瞿佳¹(), 赵玲侠¹(), 门欣¹, 孙晓宇¹, 陈锐¹, 宁硕瀛²

¹ 陕西省微生物研究所，西安 710043
² 陕西省秦岭生态安全重点实验室陕西省动物研究所，西安 710032

收稿日期:2026-01-04 修回日期:2026-04-20 出版日期:2026-06-25 发布日期:2026-06-23
通讯作者:
赵玲侠，女，1983年出生，陕西黄陵人，助理研究员，博士，研究方向：微生物资源的开发利用。通信地址：710043 陕西省西安市西影路76号陕西省微生物研究所，Tel：029-82357089，E-mail：mulanmeor@163.com。
作者简介:
瞿佳，女，1987年出生，陕西汉中人，副研究员，硕士，研究方向：微生物资源的开发利用。通信地址：710043 陕西省西安市西影路76号陕西省微生物研究所，Tel：029-82357089，E-mail：q_jia@163.com。
基金资助:
陕西省自然科学基金“绿针假单胞菌SF12防治石榴干腐病的生防机理研究”(2025JC-YBQN-229); 陕西省重点研发计划一般项目“陕西道地中药材种植基地重金属-抗生素-抗性基因污染特征分析及微生物土壤修复剂开发与示范”(2023-YBNY-236); “根结线虫微生物农药紧密帚枝霉缓释颗粒剂的创制与应用研究”(2024NC-YBXM-052); “石榴蓟马抗药性监测与绿色防控技术研究”(2024NC-YBXM-057); 陕西省创新能力支撑计划项目“陕西省微生物资源平台升级建设”(2024CX-GXPT-02); 陕西省科学院科技计划项目“陕西石榴病虫害绿色防控技术研究与应用”(2023k-11); “陕西省微生物资源平台升级建设”(2025k-39); 西安市农业技术研发项目“西安市访花昆虫资源与优势物种授粉效果研究”(23NYGG0023); “石榴果园土壤改良关键技术研究”(24NYGG0099); “石榴绿盲蝽抗药性监测与防控技术研究”(25NJSYB00042)

Complete Genome Sequencing and Analysis of Antagonistic Streptomyces caeruleatus WMF106 Against Walnut Blight

QU Jia¹(), ZHAO Lingxia¹(), MEN Xin¹, SUN Xiaoyu¹, CHEN Rui¹, NING Shuoying²

¹ Shaanxi Institute of Microbiology, Xi’an 710032
² Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an 710032

Received:2026-01-04 Revised:2026-04-20 Published:2026-06-25 Online:2026-06-23

摘要/Abstract

摘要：

核桃黑斑病是核桃生产中最严重的细菌性病害，化学防治易造成污染与抗性问题，亟需绿色高效生防资源。菌株WMF106是对核桃黑斑病菌具有较强拮抗活性的暗蓝色链霉菌(Streptomyces caeruleatus)。为进一步了解该菌株的生防遗传基础，解析其防治核桃黑斑病的分子机理，本研究对菌株WMF106进行全基因组测序与功能分析。采用二代+三代测序技术组装基因组，进行基因预测、功能注释及次级代谢产物合成基因簇挖掘。结果表明：菌株WMF106基因组由1条染色体（染色体基因组总长度10,377,577 bp，GC含量为71.16%）和2个质粒组成，共预测编码基因9253个；在NR、eggNOG、Swiss-port、KEEG、GO、CAZy、TCDB、CARD、PHI、VFDB数据库中注释到的基因分别为8981、7933、5787、2979、6426、510、1319、142、7和1507个。共鉴定出36个次级代谢产物合成基因簇，其中10个与已知抗菌物质基因簇同源性达90%~100%，包括覆盖霉素、1,3,6,8-四羟基萘、铁载体coelichelin、ε-聚赖氨酸等。基因组不含典型毒力因子，生物安全性高。本研究明确了菌株WMF106的遗传背景与生防潜力，为挖掘新型抗菌活性物质、研发核桃黑斑病生物防治制剂提供了重要基因资源与理论支撑。

关键词: 暗蓝色链霉菌, 核桃黑斑病, 全基因组测序, 基因注释, 次级代谢, 生物防治

Abstract:

Walnut blight is the most serious bacterial disease in walnut production. Chemical control is easy to cause pollution and resistance problems, and green and efficient biocontrol resources are urgently needed. As an important biocontrol agent, Streptomyces caeruleatus WMF106 exhibits good antagonistic effect on the pathogen of walnut blight. To further understand the characteristics and secondary metabolites of this actinomycete, which is beneficial for the application of antimicrobial agent in the control of the disease, the whole genome sequencing of strain WMF106 was conducted, and the sequencing data were analyzed for gene prediction, functional annotation, and analysis of secondary metabolite biosynthesis gene clusters. The results indicated that WMF106 genome consisted of one chromosomal DNA and two plasmid DNAs. The genome of chromosomal DNA was 10,377,577 bp long with the G+C content of 71.16%, encoding 9 253 protein-coding genes. Genes annotated in NR, eggNOG, Swiss-port, KEEG, GO, CAZy, TCDB, CARD, PHI, and VFDB databases numbered 8981, 7933, 5787, 2979, 6426, 510, 1319, 142, 7 and 1507, respectively. In addition, 36 biosynthetic gene clusters were identified, and several of them associated with antibacterial activity were detected, such as those responsible for the biosynthesis of collinomycin, 1,3,6,8-THN, coelichelin and ε-poly-L-lysine. The genome did not contain typical virulence factors and had high biosafety. The genetic background and biocontrol potential of strain WMF106 were clarified, which provided important genetic resources and theoretical support for the discovery of new antibacterial active substances and the development of biological control agents for walnut blight.

Key words: Streptomyces caeruleatus, walnut blight, whole genome sequencing, gene annotation, secondary metabolism, biocontrol

中图分类号:

S476.9

瞿佳, 赵玲侠, 门欣, 孙晓宇, 陈锐, 宁硕瀛. 核桃黑斑病生防链霉菌WMF106全基因组测序及分析[J]. 中国农学通报, 2026, 42(12): 144-154.

QU Jia, ZHAO Lingxia, MEN Xin, SUN Xiaoyu, CHEN Rui, NING Shuoying. Complete Genome Sequencing and Analysis of Antagonistic Streptomyces caeruleatus WMF106 Against Walnut Blight[J]. Chinese Agricultural Science Bulletin, 2026, 42(12): 144-154.

图/表 9

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特征	染色体	质粒Ⅰ	质粒Ⅱ
基因组长度/bp	10,377,577	109,814	63,717
GC content/%	71.16	69.01	69.75
CDS	9253	128	54
rRNA	18	0	0
tRNA	68	0	1
ncRNA	37	0	0
编码基因长度/bp	9,002,067	87,660	51,771
编码基因平均长度/bp	972.88	684.84	958.72

特征	染色体	质粒Ⅰ	质粒Ⅱ
基因组长度/bp	10,377,577	109,814	63,717
GC content/%	71.16	69.01	69.75
CDS	9253	128	54
rRNA	18	0	0
tRNA	68	0	1
ncRNA	37	0	0
编码基因长度/bp	9,002,067	87,660	51,771
编码基因平均长度/bp	972.88	684.84	958.72

基因簇	类型	起始位置	终止位置	基因数	最相似的已知基因簇	相似性/%
Cluster 1	T1PKS	473112	517152	34	chlorothricin	4
Cluster 2	NI-siderophore	648701	681402	28	peucechelin	30
Cluster 3	lanthipeptide-class-iii	693542	718624	19	informatipeptin	85
Cluster 4	thiopeptide	1200914	1247000	32	brasilinolide A	2
Cluster 5	betalactone	1265318	1296995	29	JBIR-76	8
Cluster 6	NRPS	1442689	1523595	62	desulfoclethramycin	28
Cluster 7	terpene	1607418	1634115	22	hopene	92
Cluster 8	hydrogen-cyanide	1727433	1740315	13	aborycin	28
Cluster 9	NRPS	1815563	1874051	37	coelichelin	100
Cluster 10	NI-siderophore	2159433	2190575	31	paulomycin	13
Cluster 11	T1PKS	2300183	2344970	30	methylenomycin A	19
Cluster 12	NAPAA	2358834	2393421	31	stenothricin	13
Cluster 13	butyrolactone	2429109	2454114	23	γ-butyrolactone	100
Cluster 14	RiPP-like	2557719	2569035	10	-	-
Cluster 15	phosphoglycolipid	2699909	2728675	23	teichomycin A1	83
Cluster 16	NI-siderophore	2841858	2871813	19	kinamycin	16
Cluster 17	NRPS	3230130	3291717	43	BD-12	17
Cluster 18	terpene	3561551	3582474	22	albaflavenone	100
Cluster 19	lassopeptide	3979785	4002344	24	siamycin I	57
Cluster 20	butyrolactone	4152386	4179447	26	pyralomicin 1a	18
Cluster 21	lanthipeptide-class-iii	4591158	4613731	27	birimositide	25
Cluster 22	lanthipeptide-class-iii	4676487	4704096	61	coumermycin A1	12
Cluster 23	T2PKS	5368148	5450890	72	collinomycin	96
Cluster 24	lanthipeptide-class-i	5913936	5940264	19	-	-
Cluster 25	NI-siderophore	6464603	6494375	29	Desferrioxamin B	100
Cluster 26	melanin	6596137	6606613	12	istamycin	5
Cluster 27	ectoine	7749935	7760339	10	ectoine	100
Cluster 28	NAPAA	8001285	8035148	28	ε-Poly-L-lysine	100
Cluster 29	terpene	8097402	8118412	18	pradimicin-A	7
Cluster 30	T3PKS	8587010	8628110	37	1,3,6,8-tetrahydroxynaphthalene	100
Cluster 31	NRPS	8632921	8690707	33	coelibactin	72
Cluster 32	T1PKS	8813467	8939812	46	salinomycin	32
Cluster 33	CDPS	9008274	9028891	22	undecylprodigiosin/metacycloprodigiosin	8
Cluster 34	NRPS	9663713	9723144	40	cysteoamide	90
Cluster 35	melanin	9925846	9936007	10	melanin	57
Cluster 36	T2PKS	10220593	10263006	43	colibrimycin	9

基因簇	类型	起始位置	终止位置	基因数	最相似的已知基因簇	相似性/%
Cluster 1	T1PKS	473112	517152	34	chlorothricin	4
Cluster 2	NI-siderophore	648701	681402	28	peucechelin	30
Cluster 3	lanthipeptide-class-iii	693542	718624	19	informatipeptin	85
Cluster 4	thiopeptide	1200914	1247000	32	brasilinolide A	2
Cluster 5	betalactone	1265318	1296995	29	JBIR-76	8
Cluster 6	NRPS	1442689	1523595	62	desulfoclethramycin	28
Cluster 7	terpene	1607418	1634115	22	hopene	92
Cluster 8	hydrogen-cyanide	1727433	1740315	13	aborycin	28
Cluster 9	NRPS	1815563	1874051	37	coelichelin	100
Cluster 10	NI-siderophore	2159433	2190575	31	paulomycin	13
Cluster 11	T1PKS	2300183	2344970	30	methylenomycin A	19
Cluster 12	NAPAA	2358834	2393421	31	stenothricin	13
Cluster 13	butyrolactone	2429109	2454114	23	γ-butyrolactone	100
Cluster 14	RiPP-like	2557719	2569035	10	-	-
Cluster 15	phosphoglycolipid	2699909	2728675	23	teichomycin A1	83
Cluster 16	NI-siderophore	2841858	2871813	19	kinamycin	16
Cluster 17	NRPS	3230130	3291717	43	BD-12	17
Cluster 18	terpene	3561551	3582474	22	albaflavenone	100
Cluster 19	lassopeptide	3979785	4002344	24	siamycin I	57
Cluster 20	butyrolactone	4152386	4179447	26	pyralomicin 1a	18
Cluster 21	lanthipeptide-class-iii	4591158	4613731	27	birimositide	25
Cluster 22	lanthipeptide-class-iii	4676487	4704096	61	coumermycin A1	12
Cluster 23	T2PKS	5368148	5450890	72	collinomycin	96
Cluster 24	lanthipeptide-class-i	5913936	5940264	19	-	-
Cluster 25	NI-siderophore	6464603	6494375	29	Desferrioxamin B	100
Cluster 26	melanin	6596137	6606613	12	istamycin	5
Cluster 27	ectoine	7749935	7760339	10	ectoine	100
Cluster 28	NAPAA	8001285	8035148	28	ε-Poly-L-lysine	100
Cluster 29	terpene	8097402	8118412	18	pradimicin-A	7
Cluster 30	T3PKS	8587010	8628110	37	1,3,6,8-tetrahydroxynaphthalene	100
Cluster 31	NRPS	8632921	8690707	33	coelibactin	72
Cluster 32	T1PKS	8813467	8939812	46	salinomycin	32
Cluster 33	CDPS	9008274	9028891	22	undecylprodigiosin/metacycloprodigiosin	8
Cluster 34	NRPS	9663713	9723144	40	cysteoamide	90
Cluster 35	melanin	9925846	9936007	10	melanin	57
Cluster 36	T2PKS	10220593	10263006	43	colibrimycin	9

核桃黑斑病生防链霉菌WMF106全基因组测序及分析

Complete Genome Sequencing and Analysis of Antagonistic Streptomyces caeruleatus WMF106 Against Walnut Blight

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类型	数据库	染色体	质粒Ⅰ	质粒Ⅱ
通用数据库	NR	8,981	118	49
	eggNOG	7,933	43	36
	Swiss-port	5,787	21	19
	KEGG	2,979	15	15
	GO	6,426	30	30
专有数据库	CAZy	510	1	0
	TCDB	1319	0	0
	CARD	142	0	0
	VFDB	7	0	0
	PHI	1507	0	0

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