Biological Characteristics and Genomic Analysis of a Novel Pathogen Strain Raoultella ornithinolytica Causing Soft Rot Disease in Konjac

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

Abstract

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

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.

Figures/Tables 11

References 52

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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