一株新的魔芋软腐病致病菌的生物学特性及基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-1253

摘要/Abstract

摘要：

目的从魔芋球茎中首次分离到1株软腐病致病菌株（Raoultella ornithinolytica Q-8，登录号：CP173279），从全基因组层面对其进行序列分析和基因功能注释，为深入研究该菌株的致病机理和对其有效防治提供理论依据。方法利用3代全基因组测序技术，通过Canu、Prodigal、RepeatMasker等软件对基因组数据进行组装和基因预测，利用KEGG、PHI-base等12个数据库进行功能注释和对比分析，并根据基因组ORF序列利用FastTree2构建系统发育树。结果 R. ornithinolytica Q-8基因组总长度为5.44 Mb，GC含量55.9%，含有4 962个编码基因、6个假基因、11个基因岛、25个rRNA、129个其他ncRNA及16种不同类型的CRISPR系统。其中有4 833个基因被注释到22个基因簇中，3 126个基因被富集到114条代谢通路中，有1 714个运输蛋白相关基因、18个抗生素耐药相关基因、1 854个病原体宿主互作相关基因和1 067个毒力因子相关基因。系统发育树分析结果表明，R. ornithinolytica Q-8与其他8株R. ornithinolytica聚在一大分支，而与已报道的2种魔芋软腐病病原菌P. carotovorum和D. chrysanthemi距离较远。结论 R. ornithinolytica Q-8是1株新的魔芋软腐病致病菌，其基因组中存在多个抗生素耐药基因和病原菌宿主互作基因，这些基因可能在其致病中发挥着重要作用。

关键词: 花魔芋, 软腐病, 解鸟氨酸拉乌尔菌, 进化树分析, 全基因组分析

Abstract:

Objective The soft rot pathogen strain (Raoultella ornithinolytica Q-8, accession number: CP173279) was first isolated from the konjac (Amorphophallus spp.) corm. Sequence analysis and gene functional annotation were conducted at the whole-genome level, which will provide a theoretical basis for in-depth research on the pathogenic mechanisms of this strain and its effective control. Method Using third-generation whole-genome sequencing technology, genomic data were assembled and genes were predicted through software tools such as Canu, Prodigal, and RepeatMasker. Functional annotation and comparative analysis were performed using 12 databases, including KEGG and PHI-base. A phylogenetic tree was constructed based on the genomic ORF sequences using FastTree2. Result The genome size of Raoultella ornithinolytica Q-8 was 5.16 Mb with a GC content of 55.9%, including 4 962 coding DNA sequences (CDSs), 6 pseudogenes, 11 genomic islands, 25 rRNA genes, 129 other ncRNAs, and 16 different types of CRISPR systems. Among these, 4 833 genes were annotated into 22 gene clusters, and 3 126 genes were enriched in 114 metabolic pathways. Additionally, there were 1 714 transporter-related genes, 18 antibiotic resistance-related genes, 1 854 pathogen-host interaction-related genes, and 1 067 virulence factor-related genes. Phylogenetic tree analysis revealed that R. ornithinolytica Q-8 and other 8 strains of R. ornithinolytica wore clustered in the same large branch while distantly related to two previously reported pathogens of konjac soft rot, P. carotovorum and D. chrysanthemi. Conclusion R. ornithinolytica Q-8 is a novel pathogenic agent causing konjac soft rot. Its genome harbors multiple antibiotic resistance genes and pathogen-host interaction genes, which are likely to play crucial roles in its virulence mechanisms.

Key words: Amorphophallus konjac K. Koch, soft rot, Raoultella ornithinolytica, phylogenetic tree analysis, whole genome analysis

刘长命, 张新悦, 杨昕萌, 刘阳, 李玥涵, 汪可清. 一株新的魔芋软腐病致病菌的生物学特性及基因组分析[J]. 生物技术通报, 2026, 42(1): 294-304.

LIU Chang-ming, ZHANG Xin-yue, YANG Xin-meng, LIU Yang, LI Yue-han, WANG Ke-qing. Biological Characteristics and Genomic Analysis of a Novel Pathogen Strain Raoultella ornithinolytica Causing Soft Rot Disease in Konjac[J]. Biotechnology Bulletin, 2026, 42(1): 294-304.

图/表 11

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样本编号 Sample No.	采样地点 Sampling location	经度 Longitude （E）	纬度 Latitude （N）	海拔 Elevation （m）
1	丹凤县南丈沟村 Nanzhanggou village， Danfeng county	110°60′23″	33°16′81″	572
2	丹凤县南丈沟村 Nanzhanggou village， Danfeng county	110°59′70″	33°16′71″	560
3	山阳县阳河村 Yanghe village， Shangyang county	110°22′38″	34°47′56″	770
4	山阳县阳河村 Yanghe village， Shangyang county	110°22′62″	34°47′65″	756
5	商南县小河村 Xiaohe village， Shangnan county	110°46′22″	33°47′46″	438
6	商南县小河村 Xiaohe village， Shangnan county	110°46′25″	33°47′44″	430

样本编号 Sample No.	采样地点 Sampling location	经度 Longitude （E）	纬度 Latitude （N）	海拔 Elevation （m）
1	丹凤县南丈沟村 Nanzhanggou village， Danfeng county	110°60′23″	33°16′81″	572
2	丹凤县南丈沟村 Nanzhanggou village， Danfeng county	110°59′70″	33°16′71″	560
3	山阳县阳河村 Yanghe village， Shangyang county	110°22′38″	34°47′56″	770
4	山阳县阳河村 Yanghe village， Shangyang county	110°22′62″	34°47′65″	756
5	商南县小河村 Xiaohe village， Shangnan county	110°46′22″	33°47′46″	438
6	商南县小河村 Xiaohe village， Shangnan county	110°46′25″	33°47′44″	430

菌株 Strain	基因组大小 Genome length （bp）	编码基因 Coding genes	GC 含量 GC content （%）	假基因 Pseudo genes	rRNA	tRNA	ncRNAs	收集日期 Collecting date	来源 Source	来源地 Source location
Q-8	5 440 241	4 962	55.9	6	25	87	129	2022.04	魔芋 Konjac	中国商洛 Shangluo， China
NY1	5 592 869	5 195	55.5	118	25	85	12	2019.08	尿液 Urine	中国济南 Jinan， China
GSH0205-8M-1	5 490 896	5 540	54.7	118	25	82	11	2019.02	污水处理厂出水 Wastewater treatment plant effluent	日本东京 Tokyo， Japan
FDAARGOS 431	5 633 990	5 600	55.5	225	25	85	12	2015.07	病人直肠 The patient’s rectum	加拿大不列颠哥伦比亚 British Columbia， Canada
SECR20-0777	5 460 546	5 088	56.0	64	25	85	13	2020.03	碳青霉烯类耐药肠杆菌科细菌感染人直肠 CRE infection on human rectal	韩国首尔 Seoul， Korea

菌株 Strain	基因组大小 Genome length （bp）	编码基因 Coding genes	GC 含量 GC content （%）	假基因 Pseudo genes	rRNA	tRNA	ncRNAs	收集日期 Collecting date	来源 Source	来源地 Source location
Q-8	5 440 241	4 962	55.9	6	25	87	129	2022.04	魔芋 Konjac	中国商洛 Shangluo， China
NY1	5 592 869	5 195	55.5	118	25	85	12	2019.08	尿液 Urine	中国济南 Jinan， China
GSH0205-8M-1	5 490 896	5 540	54.7	118	25	82	11	2019.02	污水处理厂出水 Wastewater treatment plant effluent	日本东京 Tokyo， Japan
FDAARGOS 431	5 633 990	5 600	55.5	225	25	85	12	2015.07	病人直肠 The patient’s rectum	加拿大不列颠哥伦比亚 British Columbia， Canada
SECR20-0777	5 460 546	5 088	56.0	64	25	85	13	2020.03	碳青霉烯类耐药肠杆菌科细菌感染人直肠 CRE infection on human rectal	韩国首尔 Seoul， Korea

CRISPR编号 CRISPR ID	起始位置 Start	结束位置 End	重复次数 Repeat number	平均重复长度 Average repeat length （bp）	间隔序列数量 Spacer number	平均间隔序列长度 Average spacer length （bp）
CRISPR.1	347 753	348 100	8	26	7	20
CRISPR.2	1 100 503	1 100 601	2	33	1	33
CRISPR.3	1 196 948	1 197 054	3	19	2	25
CRISPR.4	2 464 743	2 464 894	3	38	2	19
CRISPR.5	2 595 049	2 595 128	2	26	1	28
CRISPR.6	2 595 022	2 595 269	5	26	4	29
CRISPR.7	2 901 354	2 901 775	9	30	8	19
CRISPR.8	3 255 068	3 255 128	2	21	1	19
CRISPR.9	3 316 575	3 316 825	4	35	3	37
CRISPR.10	3 608 294	3 608 756	7	31	6	41
CRISPR.11	3 752 358	3 752 470	2	32	1	49
CRISPR.12	3 969 172	3 969 472	4	37	3	51
CRISPR.13	4 705 327	4 705 595	5	38	4	19
CRISPR.14	4 846 212	4 846 348	3	33	2	19
CRISPR.15	4 853 717	4 853 915	3	31	2	53
CRISPR.16	5 039 222	5 039 506	5	21	4	45