Pub Date : 2024-01-12DOI: 10.1094/phytofr-09-23-0124-a
Wan-Zhen Luo, Hengguang Zhu, Hong-Yue Qi, Jiangqing Song, Dan-Dan Zhang, X. Dai, Mai-He-Mu-Ti Mijiti, Jiemin Chen, Dongfei Han, Dan Wang
The KRS022 was isolated from the rhizosphere soil of a healthy plant in a pathogen-infested cotton field in Xinjiang, China. Previous studies have demonstrated that KRS022 possesses the ability to trigger plant immune responses, inhibit the growth of various pathogenic fungi, including Verticillium dahliae, and promote plant growth. The antagonistic properties of KRS022 primarily stem from its bioactive metabolites. In this study, the high-quality genome of KRS022 was obtained. The KRS022 genome consists of a chromosome of 6,369,026 bp with 67.09% GC content, possesses 5,830 ORFs, of which 5,186 genes were annotated, and 119 ncRNA genes. Additionally, eleven gene clusters of secondary metabolites biosynthesis were predicted, involving in PKS, arylpolyene, NAGGN, betalactone, ranthipeptide, RIPP-like, redox-cofactor, and NRPS clusters. It could be useful to explore the biocontrol potential of P. tohonis, implying promising application of KRS022 in biological control.
{"title":"Complete Genome Resource of a Fungal Antagonistic Strain: Pseudomonas tohonis","authors":"Wan-Zhen Luo, Hengguang Zhu, Hong-Yue Qi, Jiangqing Song, Dan-Dan Zhang, X. Dai, Mai-He-Mu-Ti Mijiti, Jiemin Chen, Dongfei Han, Dan Wang","doi":"10.1094/phytofr-09-23-0124-a","DOIUrl":"https://doi.org/10.1094/phytofr-09-23-0124-a","url":null,"abstract":"The KRS022 was isolated from the rhizosphere soil of a healthy plant in a pathogen-infested cotton field in Xinjiang, China. Previous studies have demonstrated that KRS022 possesses the ability to trigger plant immune responses, inhibit the growth of various pathogenic fungi, including Verticillium dahliae, and promote plant growth. The antagonistic properties of KRS022 primarily stem from its bioactive metabolites. In this study, the high-quality genome of KRS022 was obtained. The KRS022 genome consists of a chromosome of 6,369,026 bp with 67.09% GC content, possesses 5,830 ORFs, of which 5,186 genes were annotated, and 119 ncRNA genes. Additionally, eleven gene clusters of secondary metabolites biosynthesis were predicted, involving in PKS, arylpolyene, NAGGN, betalactone, ranthipeptide, RIPP-like, redox-cofactor, and NRPS clusters. It could be useful to explore the biocontrol potential of P. tohonis, implying promising application of KRS022 in biological control.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"46 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139533225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-03DOI: 10.1094/phytofr-10-23-0139-a
X. A, Le Mei, Yayun Yang, Cui-feng Tang, Feifei Zhang, Chao Dong, Bin Wang, Pengcheng Liu, Xifeng Chen, Bojun Ma, Luyuan Dai
Xanthomonas oryzae are destructive phytopathogens in rice production, and also an important model system for studying the interaction between plants and bacterial pathogens. Here, we report the isolation and complete genome sequence of a X. oryzae strain YXol-1, and through the identification of transcription activator-like effectors (TALEs) and whole genome based phylogenetic analysis, we confirmed YXol-1 belongs to a rarely reported type of X. oryzae pathovar named as X. oryzae pv. leersiae (Xol). The present work enriched the genetic resources of Xol for studying the evolution of X. oryzae strains and can contribute to a better understanding of Xol-host interaction.
{"title":"Complete Genome Resource of Xanthomonas oryzae pv. leersiae Strain YXol-1 Isolated From Plateau Japonica Rice in Yunnan Province, China","authors":"X. A, Le Mei, Yayun Yang, Cui-feng Tang, Feifei Zhang, Chao Dong, Bin Wang, Pengcheng Liu, Xifeng Chen, Bojun Ma, Luyuan Dai","doi":"10.1094/phytofr-10-23-0139-a","DOIUrl":"https://doi.org/10.1094/phytofr-10-23-0139-a","url":null,"abstract":"Xanthomonas oryzae are destructive phytopathogens in rice production, and also an important model system for studying the interaction between plants and bacterial pathogens. Here, we report the isolation and complete genome sequence of a X. oryzae strain YXol-1, and through the identification of transcription activator-like effectors (TALEs) and whole genome based phylogenetic analysis, we confirmed YXol-1 belongs to a rarely reported type of X. oryzae pathovar named as X. oryzae pv. leersiae (Xol). The present work enriched the genetic resources of Xol for studying the evolution of X. oryzae strains and can contribute to a better understanding of Xol-host interaction.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"4 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139389495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-17DOI: 10.1094/phytofr-08-23-0114-a
Jiangqing Song, Jiemin Chen, Dan-Dan Zhang, Ran Li, Zhiqiang Kong, Hengguang Zhu, X. Dai, Dongfei Han, Dan Wang
Bacillus subtilis, a gram-positive bacterium commonly found in soil, is an excellent organism for plant biocontrol. The B. subtilis KRS015, an endophyte isolated from the seed of Gossypium hirsutum "Zhongzhimian No. 2", has been proven as its antagonistic activity against diverse fungal pathogens of plants, including Verticillium dahliae, a fungal pathogen of Verticillium wilt in various plants such as cotton. Here, we report the complete genome sequence of B. subtilis KRS015. The size of the KRS015 genome is 4,331,506 bp. Fifteen gene clusters for antibiotics and secondary metabolites, and 412 genes involved in plant bacterial interactions were identified in this genome. These findings qualified the potential of B. subtilis KRS015 as a biocontrol agent and may help reveal the molecular basis of its antagonistic mechanisms.
{"title":"Genome Resource of Bacillus subtilis KRS015, a Potential Biocontrol Agent for Verticillium dahliae","authors":"Jiangqing Song, Jiemin Chen, Dan-Dan Zhang, Ran Li, Zhiqiang Kong, Hengguang Zhu, X. Dai, Dongfei Han, Dan Wang","doi":"10.1094/phytofr-08-23-0114-a","DOIUrl":"https://doi.org/10.1094/phytofr-08-23-0114-a","url":null,"abstract":"Bacillus subtilis, a gram-positive bacterium commonly found in soil, is an excellent organism for plant biocontrol. The B. subtilis KRS015, an endophyte isolated from the seed of Gossypium hirsutum \"Zhongzhimian No. 2\", has been proven as its antagonistic activity against diverse fungal pathogens of plants, including Verticillium dahliae, a fungal pathogen of Verticillium wilt in various plants such as cotton. Here, we report the complete genome sequence of B. subtilis KRS015. The size of the KRS015 genome is 4,331,506 bp. Fifteen gene clusters for antibiotics and secondary metabolites, and 412 genes involved in plant bacterial interactions were identified in this genome. These findings qualified the potential of B. subtilis KRS015 as a biocontrol agent and may help reveal the molecular basis of its antagonistic mechanisms.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"69 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139176330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-11DOI: 10.1094/phytofr-10-23-0137-r
Hope Renfroe-Becton, Jonathan Croft, Charles Davis, Joe Varn, Albert Culbreath, David Langston, Dan Anco
Late leaf spot, caused by Nothopassalora personata, is an economically important disease of peanut which routinely requires preventative fungicide application. The objectives of this study were to quantify the risk of phenotypic fungicide resistance and potential cross-resistance among Nothopassalora personata populations. A total of 59 samples of N. personata isolates were collected from 28 grower or research fields in SC, GA, and VA. Phenotypic resistance of isolates was evaluated against 14 fungicides and a nontreated control, with active ingredients from the quinone outside inhibitor (QoI), demethylation inhibitor (DMI), and succinate-dehydrogenase inhibitor (SDHI) classes. Overall, lesion development ≥ 15% was observed with nearly all isolates for at least one of the active ingredients tested. Correlations between active ingredients, penthiopyrad and pydiflumetofen, as well as bixafen plus flutriafol and pydiflumetofen, and their lesion development risk indicates potential N. personata populations with SDHI cross-resistance. While these data do not confirm the presence of genetic resistance markers, results paired with observed reduced efficacy in the field reinforce the strong need for an integrated approach in managing late leaf spot. In areas with high probabilities for resistance to several modes of action, longer rotations out of peanut, varieties with greater levels of resistance, earlier planting, and continued incorporation of active ingredients with multi-site mode of action in fungicide programs are advised for preserving fungicide efficacy or reducing selection pressure.
{"title":"Phenotypic fungicide resistance and cross-resistance among Nothopassalora personata populations","authors":"Hope Renfroe-Becton, Jonathan Croft, Charles Davis, Joe Varn, Albert Culbreath, David Langston, Dan Anco","doi":"10.1094/phytofr-10-23-0137-r","DOIUrl":"https://doi.org/10.1094/phytofr-10-23-0137-r","url":null,"abstract":"Late leaf spot, caused by Nothopassalora personata, is an economically important disease of peanut which routinely requires preventative fungicide application. The objectives of this study were to quantify the risk of phenotypic fungicide resistance and potential cross-resistance among Nothopassalora personata populations. A total of 59 samples of N. personata isolates were collected from 28 grower or research fields in SC, GA, and VA. Phenotypic resistance of isolates was evaluated against 14 fungicides and a nontreated control, with active ingredients from the quinone outside inhibitor (QoI), demethylation inhibitor (DMI), and succinate-dehydrogenase inhibitor (SDHI) classes. Overall, lesion development ≥ 15% was observed with nearly all isolates for at least one of the active ingredients tested. Correlations between active ingredients, penthiopyrad and pydiflumetofen, as well as bixafen plus flutriafol and pydiflumetofen, and their lesion development risk indicates potential N. personata populations with SDHI cross-resistance. While these data do not confirm the presence of genetic resistance markers, results paired with observed reduced efficacy in the field reinforce the strong need for an integrated approach in managing late leaf spot. In areas with high probabilities for resistance to several modes of action, longer rotations out of peanut, varieties with greater levels of resistance, earlier planting, and continued incorporation of active ingredients with multi-site mode of action in fungicide programs are advised for preserving fungicide efficacy or reducing selection pressure.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"71 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139183475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dickeya fangzhongdai ZXC1 is a newly identified highly virulent causal agent of taro bacterial soft rot disease isolated from the taro sample showing typical soft rot symptoms at Shaoguan, Guangdong Province, China. The pathogen produces plant cell wall degrading enzymes which macerate the taro tube tissues. In this study, we report the whole genome sequencing analysis of strain ZXC1. The results showed that strain ZXC1 has one circular DNA chromosome of 5,129,951 bp with 56.59% G+C content. In addition to sharing a conserved zms gene cluster that encodes the genes for biosynthesis of phytotoxin zeamines, and 11 copies of predicted pectate lyases genes, the strain ZXC1 genome contains more prophage loci and higher number of type IV secretion system (T4SS) and type IV secretion system (T6SS) gene clusters than the D. fangzhongdai strains isolated from pears or phalaenopsis, which may account for its strong virulence phenotype. The data from this study present a valuable resource for elucidation of the pathogenic mechanisms of D. fangzhongdai, and may aid in developing new disease control approaches to safeguard taro production.
Dickeya fangzhongdai ZXC1是从中国广东省韶关市出现典型软腐症状的芋头样品中分离出来的一种新发现的芋头细菌性软腐病高致病性病原菌。该病原菌能产生植物细胞壁降解酶，使芋头管组织浸渍。本研究报告了对菌株 ZXC1 的全基因组测序分析。结果表明，菌株 ZXC1 有一个 5,129,951 bp 的环状 DNA 染色体，G+C 含量为 56.59%。与分离自梨或蝴蝶兰的方中快菌株相比，菌株 ZXC1 基因组除了共享一个保守的 zms 基因簇（编码植物毒素玉米素生物合成基因）和 11 个拷贝的预测酪酸酶基因外，还含有更多的噬菌体位点和更多的 IV 型分泌系统（T4SS）和 IV 型分泌系统（T6SS）基因簇，这可能是其具有强烈毒力表型的原因。这项研究的数据为阐明方中莱氏菌的致病机制提供了宝贵的资源，并可能有助于开发新的病害控制方法，以保障芋头生产。
{"title":"Genome sequence resource of a taro bacterial soft rot pathogen Dickeya fangzhongdai ZXC1","authors":"Zhongqiao Chen, Weihan Gu, Congcong Xie, Huagui Gao, Shufen Huang, Lian-hui Zhang, L. Liao","doi":"10.1094/phytofr-07-23-0090-a","DOIUrl":"https://doi.org/10.1094/phytofr-07-23-0090-a","url":null,"abstract":"Dickeya fangzhongdai ZXC1 is a newly identified highly virulent causal agent of taro bacterial soft rot disease isolated from the taro sample showing typical soft rot symptoms at Shaoguan, Guangdong Province, China. The pathogen produces plant cell wall degrading enzymes which macerate the taro tube tissues. In this study, we report the whole genome sequencing analysis of strain ZXC1. The results showed that strain ZXC1 has one circular DNA chromosome of 5,129,951 bp with 56.59% G+C content. In addition to sharing a conserved zms gene cluster that encodes the genes for biosynthesis of phytotoxin zeamines, and 11 copies of predicted pectate lyases genes, the strain ZXC1 genome contains more prophage loci and higher number of type IV secretion system (T4SS) and type IV secretion system (T6SS) gene clusters than the D. fangzhongdai strains isolated from pears or phalaenopsis, which may account for its strong virulence phenotype. The data from this study present a valuable resource for elucidation of the pathogenic mechanisms of D. fangzhongdai, and may aid in developing new disease control approaches to safeguard taro production.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"25 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139183959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-11DOI: 10.1094/phytofr-10-23-0136-r
N. Subedi, Tabitha Cowell, Matthew L Cope-Arguello, P. Paul, G. Cellier, Hashem Bkayrat, Nicholas Bonagura, Agela Cadatal, Rachel Chen, Ariana Enriquez, Rama Parasar, Lisa Repetto, Aracely Hernandez Rivas, Mahnoor Shahbaz, Kaitlin White, Tiffany Lowe-Power, S. A. Miller
In South Asia, bacterial wilt pathogens in the Ralstonia solanacearum species complex (RSSC) impose major constraints on eggplant, tomato, and pepper production. To improve the efficacy of bacterial wilt management, the goals of this study were to (1) conduct a survey of RSSC pathogens in Bangladesh and Nepal, (2) characterize the genetic diversity of these isolates, and (3) screen 37 tomato, eggplant, and pepper accessions for resistance to six representative isolates from South Asia. We isolated 99 isolates from Bangladesh and 20 isolates from Nepal and determined that all are phylotype I isolates of the Ralstonia pseudosolanacearum species. We sequenced and assembled draft genomes for 25 isolates. Phylogenomic analyses suggest that there is a wide diversity of endemic phylotype I isolates in South Asia, and possible introductions of two clonal phylotype I lineages into Bangladesh and Nepal. We contextualize our newly described isolates based on prior reports of RSSC diversity in South Asia and global reports of RSSC pathogens on eggplant and pepper. Greenhouse trials revealed multiple tomato, eggplant, and pepper accessions that exhibit promising levels of resistance to six phylotype I isolates from South Asia.
{"title":"Characterization of Ralstonia pseudosolanacearum diversity and screening tomato, pepper, and eggplant resistance to manage bacterial wilt in South Asia","authors":"N. Subedi, Tabitha Cowell, Matthew L Cope-Arguello, P. Paul, G. Cellier, Hashem Bkayrat, Nicholas Bonagura, Agela Cadatal, Rachel Chen, Ariana Enriquez, Rama Parasar, Lisa Repetto, Aracely Hernandez Rivas, Mahnoor Shahbaz, Kaitlin White, Tiffany Lowe-Power, S. A. Miller","doi":"10.1094/phytofr-10-23-0136-r","DOIUrl":"https://doi.org/10.1094/phytofr-10-23-0136-r","url":null,"abstract":"In South Asia, bacterial wilt pathogens in the Ralstonia solanacearum species complex (RSSC) impose major constraints on eggplant, tomato, and pepper production. To improve the efficacy of bacterial wilt management, the goals of this study were to (1) conduct a survey of RSSC pathogens in Bangladesh and Nepal, (2) characterize the genetic diversity of these isolates, and (3) screen 37 tomato, eggplant, and pepper accessions for resistance to six representative isolates from South Asia. We isolated 99 isolates from Bangladesh and 20 isolates from Nepal and determined that all are phylotype I isolates of the Ralstonia pseudosolanacearum species. We sequenced and assembled draft genomes for 25 isolates. Phylogenomic analyses suggest that there is a wide diversity of endemic phylotype I isolates in South Asia, and possible introductions of two clonal phylotype I lineages into Bangladesh and Nepal. We contextualize our newly described isolates based on prior reports of RSSC diversity in South Asia and global reports of RSSC pathogens on eggplant and pepper. Greenhouse trials revealed multiple tomato, eggplant, and pepper accessions that exhibit promising levels of resistance to six phylotype I isolates from South Asia.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"27 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139184047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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