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Genomic features of the host-specific fungal biocontrol agent Ramularia crupinae approved for the management of the federally noxious weed Crupina vulgaris 被批准用于管理联邦有害杂草 Crupina vulgaris 的寄主特异性真菌生物控制剂 Ramularia crupinae 的基因组特征
Pub Date : 2023-11-29 DOI: 10.1094/phytofr-10-23-0138-sc
Matthew A. Tancos, Michael Robert Fulcher
Ramularia crupinae is a novel host-specific fungal pathogen of the invasive rangeland weed common crupina (Crupina vulgaris). The foliar and stem blighting pathogen was originally identified in France and has been approved by the United States Department of Agriculture – Animal and Plant Health Inspection Service as the first biological control agent for the management of common crupina in the western United States. In this study, a chromosome-level genome assembly of R. crupinae 00-010 was performed using PacBio sequencing technology. The assembly had a total size of 37.9 Mb distributed across 14 (telomere to telomere) chromosomes, with a GC content of 47.6%. The genome encoded 10,159 protein-coding genes with 890 predicted secreted proteins that comprised both unique and conserved canonical pathogen effectors. Genome comparisons with closely related pathogen species in the family Mycosphaerellaceae demonstrated family-wide orthologous effector groups and Ramularia specific orthogroups. This new reference sequence is a valuable genomic tool that will assist in characterizing Ramularia-Crupina interactions and increase our understanding of Ramularia pathogenicity on both crops and weeds.
Ramularia crupinae 是入侵性牧场杂草普通蟋蟀草(Crupina vulgaris)的一种新型寄主特异性真菌病原体。这种叶枯病和茎枯病病原体最初是在法国发现的,并已被美国农业部动植物卫生检验局批准为第一种生物防治药剂,用于美国西部普通蟋蟀草的管理。本研究使用 PacBio 测序技术对 R. crupinae 00-010 进行了染色体组水平的基因组组装。该基因组的总大小为 37.9 Mb,分布在 14 条(端粒到端粒)染色体上,GC 含量为 47.6%。基因组编码了 10,159 个蛋白编码基因,其中有 890 个预测分泌蛋白,包括独特的和保守的典型病原体效应因子。与真菌磷脂菌科近缘病原体物种的基因组比较显示了整个家族的同源效应物群和Ramularia特有的同源群。这一新的参考序列是一种宝贵的基因组工具,将有助于确定 Ramularia-Crupina 相互作用的特征,并加深我们对 Ramularia 对作物和杂草致病性的了解。
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引用次数: 0
Fatty acid methyl ester profiling of Californian Xylella fastidiosa strains 加利福尼亚 Xylella fastidiosa 菌株的脂肪酸甲酯分析
Pub Date : 2023-11-27 DOI: 10.1094/phytofr-09-23-0120-sc
Christopher Wallis, Jianchi Chen
Xylella fastidiosa ssp. fastidiosa (Xff) is the causal agent of Pierce’s disease of grapevine, a management-intensive and potentially deadly disease. However, different stains and other subspecies, such as Xylella fastidiosa ssp. multiplex (Xfm), exist in the same regions and vary in capacity to cause disease. All strains differ in the fatty acids that comprise cell membranes, as these would allow adaptations to specific host microenvironments. Therefore, studies were initiated to observe the fatty acid profiles of different Californian Xf isolates via fatty acid methyl ester (FAME) analysis. Observations revealed that the four Xff strains had similar FAME profiles that were distinct from those of the three Xfm strains, even in isolates that originated from the same host plant species. These data show consistent differences between Xff and Xfm strains, and demonstrate the potential that FAME profiling has for Xylella subspecies identification of novel isolates.
Xylella fastidiosa ssp. fastidiosa(Xff)是葡萄皮尔斯氏病的病原菌,这是一种管理密集型且可能致命的疾病。然而,同一地区还存在不同的染色种和其他亚种,如 Xylella fastidiosa ssp. multiplex (Xfm),它们的致病能力也各不相同。所有菌株组成细胞膜的脂肪酸都不相同,因为这些脂肪酸可以适应特定的宿主微环境。因此,研究人员开始通过脂肪酸甲酯(FAME)分析来观察不同加州 Xf 分离物的脂肪酸谱。观察结果表明,四株 Xff 菌株的脂肪酸甲酯谱与三株 Xfm 菌株的脂肪酸甲酯谱相似,甚至在源自相同寄主植物物种的分离株中也有区别。这些数据表明 Xff 菌株和 Xfm 菌株之间存在一致的差异,并证明了 FAME 分析在鉴定新分离株的 Xylella 亚种方面的潜力。
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引用次数: 0
Genome sequence resource of Streptomyces scabiei LBUM848, a model strain causing common scab of potato 引起马铃薯常见疮痂病的模式菌株--疮痂病链霉菌 LBUM848 的基因组序列资源
Pub Date : 2023-11-24 DOI: 10.1094/phytofr-11-23-0147-a
A. Biessy, Renée J. St-Onge, Mélanie J. Cadieux, M. Ciotola, M. Filion
Potato common scab is a deleterious bacterial disease caused by multiple Streptomyces species. In this paper, we report the high-quality genome sequence of the scab-causing strain Streptomyces scabiei LBUM848, which was isolated from a scab-infected potato tuber harvested in Bloomfield (New-Brunswick, Canada). LBUM848 has been used as a model strain for more than a decade in our laboratory to study the interaction between plant-beneficial phenazine-producing Pseudomonas spp. and scab-causing Streptomyces spp.
马铃薯普通疮痂病是一种由多种链霉菌引起的有害细菌性疾病。本文报告了从布卢姆菲尔德(加拿大新不伦瑞克省)收获的受疮痂病感染的马铃薯块茎中分离出的致疮痂病链霉菌株 LBUM848 的高质量基因组序列。十多年来,我们实验室一直将 LBUM848 作为模式菌株,用于研究对植物有益的产酚假单胞菌属(Pseudomonas)与引起疮痂病的链霉菌属(Streptomyces)之间的相互作用。
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引用次数: 0
Genomic Resource Insights into Strain WZ-12: An Antimicrobial-Producing Streptomyces Isolate from Star Anise Rhizosphere Soil WZ-12 菌株基因组资源透视:八角根瘤土壤中的抗菌链霉菌分离物
Pub Date : 2023-11-21 DOI: 10.1094/phytofr-08-23-0117-a
Jieming Pan, Xiaoshan Geng, Yulin Zhu, Qin Liu
Strain WZ-12, isolated from the rhizosphere soil of star anise trees, exhibits significant antifungal efficacy against a variety of fungi, including Colletotrichum horii, the pathogenic fungus responsible for anthracnose in star anise. Based on 16S rRNA gene sequencing and phylogenetic analysis, the strain was identified as a member of the Streptomyces genus. The genome of WZ-12 comprises a linear chromosome of 9,169,400 bp and a plasmid of 378,325 bp, possessing a G + C content of 71.12%. Of note, the genome encompasses 8,172 protein-coding genes, 21 rRNA genes, 74 tRNA genes, and 89 other non-coding RNA genes. The COG, Swiss-Prot, GO, KEGG, and NR databases annotated up to 79.17%, 50.50%, 13.17%, 37.51%, and 90.43% of potential genes, respectively. Remarkably, the genome hosts 175 antimicrobial resistance genes and 33 secondary metabolite gene clusters that likely contribute to the biosynthesis of diverse bioactive compounds such as antibiotics and agents with antitumor, antioxidant, immunosuppressive, anti-inflammatory, or stress tolerance properties. These findings highlight the potential of WZ-12 as a promising source of novel bioactive molecules and suggest its significant value as a valuable resource for developing innovative antimicrobial agents.
从八角树根瘤土壤中分离出的菌株 WZ-12 对多种真菌具有显著的抗真菌功效,包括八角炭疽病的致病真菌 Colletotrichum horii。根据 16S rRNA 基因测序和系统进化分析,该菌株被确定为链霉菌属的成员。WZ-12 的基因组由 9,169,400 bp 的线性染色体和 378,325 bp 的质粒组成,G+C含量为 71.12%。值得注意的是,该基因组包含 8172 个蛋白质编码基因、21 个 rRNA 基因、74 个 tRNA 基因和 89 个其他非编码 RNA 基因。COG、Swiss-Prot、GO、KEGG 和 NR 数据库分别注释了 79.17%、50.50%、13.17%、37.51% 和 90.43% 的潜在基因。值得注意的是,该基因组包含 175 个抗菌药耐药性基因和 33 个次级代谢物基因簇,这些基因簇可能有助于多种生物活性化合物的生物合成,如抗生素和具有抗肿瘤、抗氧化、免疫抑制、抗炎或抗应激特性的制剂。这些发现凸显了 WZ-12 作为新型生物活性分子来源的潜力,并表明它作为开发创新抗菌剂的宝贵资源具有重大价值。
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引用次数: 0
Chromosome-Scale Genome Resource for Two Neopestalotiopsis spp. Isolates with Different Virulence in Strawberry (Fragaria × ananassa) 草莓(Fragaria × ananassa)中具有不同毒力的两种 Neopestalotiopsis 株系的染色体级基因组资源
Pub Date : 2023-11-21 DOI: 10.1094/phytofr-08-23-0110-a
Hyeondae Han, Yoon Jeong Jang, Youngjae Oh, M. Marin, J. Huguet-Tapia, Natalia A. Peres, Seonghee Lee
Several Neopestalotiopsis spp. have been reported to affect strawberry worldwide. Here, we sequenced two isolates of Neopestalotiopsis 19-02 (high virulent) and 13-481 (moderate virulent) recovered from commercial strawberry fields in Florida and generated chromosome-scale assemblies using Oxford Nanopore Technologies and Illumina platforms. Each genome assembly for 19-02 and 13-481 contained putative telomere sequences at the 5’ and 3’ ends. By analyzing the collinearity of the two newly assembled genomes and verifying the conserved telomere sequence at the end of each chromosome, we confirmed that the genome of Neopestalotiopsis spp. consists of seven basic chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed 98.5% of conserved core genes for both genome assemblies, 19-02 and 13-481. Phylogenetic analysis with internal transcribed spacer (ITS), beta-tubulin (β-tub), and translation elongation factor (tef1) regions obtained from the assemblies 19-02 and 13-481 demonstrated that the highly virulent isolate 19-02 is phylogenetically distinct from moderate virulent N. rosae 13-481. Comparative genome analysis of the high-quality reference genome assemblies provided in this study will facilitate the identification of genomic regions responsible for the different virulence of Neopestalotiopsis pathogen to strawberry.
据报道,全球有几种新孢霉属(Neopestalotiopsis)会影响草莓。在这里,我们对从佛罗里达州商业草莓田中分离出的两株Neopestalotiopsis 19-02(高致病力)和13-481(中等致病力)进行了测序,并利用牛津纳米孔技术公司(Oxford Nanopore Technologies)和Illumina平台生成了染色体组规模的组合。19-02 和 13-481 的每个基因组组装都包含 5' 和 3' 端的假定端粒序列。通过分析这两个新组装基因组的共线性并验证每条染色体末端的保守端粒序列,我们证实新栉水母(Neopestalotiopsis spp.)的基因组由七条基本染色体组成。通用单拷贝同源物基准(BUSCO)分析表明,在 19-02 和 13-481 两个基因组组装中,98.5% 的核心基因是保守的。利用从 19-02 和 13-481 基因组中获得的内部转录间隔区(ITS)、β-微管蛋白(β-tub)和翻译伸长因子(tef1)区域进行的系统发生学分析表明,高致病性分离株 19-02 在系统发生学上有别于中等致病性的 N. rosae 13-481。对本研究提供的高质量参考基因组组装进行比较基因组分析,将有助于确定导致草莓新孢霉属病原体不同毒力的基因组区域。
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引用次数: 0
Perspectives towards collective action for pest and disease management in vineyards in the western US 美国西部葡萄园病虫害管理集体行动展望
Pub Date : 2023-11-15 DOI: 10.1094/phytofr-07-23-0082-r
Sarah R. Lowder, Michelle M. Moyer, Monica L. Cooper, Jay Pscheidt, Walter F. Mahaffee
An individual grower’s response to pests and diseases in their vineyard can have consequences for an entire growing region. Collective action strategies can help align grower responses to achieve better regional disease control. Ways in which we identify, approach, and address manager opinions regarding cooperative management efforts influences the success of collective action strategies. A Q-method survey was conducted to investigate the adoption obstacles of wine grape growers to regionally collective actions for managing pests and diseases. Qualitative information from the western US (n = 17 participants) was used to generate 36 statements describing opinions on collective management action and general disease management. A second set of grape producers (n = 59) were asked to rank these statements relative to each other. Participants perceived that collective management action would be worth the extra associated time or costs. Four prominent archetypal perspectives arose from the Q-method analysis explaining 66% of the variance in expressed opinions. Archetypes were termed, “The Cooperators" (14 of 59), “The Quasi-Individualists” (9 of 59), “The Mid-Level Pragmatists” (8 of 59), and “The Bottom-Line Focused” (5 of 59). These groups were split across the demographic information collected; archetypes explained more variation between responses than demographic information. Overall, participants were likely to agree that cooperation was important, but they were more concerned about their individual vineyard economic and crop health concerns. Thus, suggesting that if outreach professionals want to increase the likelihood of grape grower participate in collective pest management actions, they should emphasize the individual benefits of participation.
单个种植者对葡萄园病虫害的应对措施可能会影响整个种植区。集体行动策略有助于调整种植者的应对措施,从而实现更好的区域病虫害控制。我们如何识别、接近和处理管理者对合作管理的意见,会影响集体行动策略的成功与否。为调查酿酒葡萄种植者采用区域性集体行动管理病虫害的障碍,我们开展了一项 Q 法调查。来自美国西部的定性信息(n = 17 名参与者)被用来生成 36 份陈述,描述对集体管理行动和一般病害管理的看法。第二组葡萄生产者(n = 59)被要求对这些陈述进行相对排序。参与者认为,集体管理行动值得付出额外的时间或成本。通过 Q 方法分析,得出了四个突出的原型观点,解释了 66% 的意见表达差异。这些原型被称为 "合作者"(59 人中有 14 人)、"准个人主义者"(59 人中有 9 人)、"中层实用主义者"(59 人中有 8 人)和 "注重底线者"(59 人中有 5 人)。这些组别在所收集的人口信息中各占一半;原型比人口信息更能解释不同回答之间的差异。总体而言,参与者可能同意合作很重要,但他们更关心各自葡萄园的经济和作物健康问题。因此,如果外联专业人员希望提高葡萄种植者参与集体病虫害管理行动的可能性,他们就应该强调参与的个人利益。
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引用次数: 0
A Genome Sequence Resource of Diaporthe nobilis Causing Kiwifruit Rot 猕猴桃腐烂病致病菌 Diaporthe nobilis 的基因组序列资源
Pub Date : 2023-11-15 DOI: 10.1094/phytofr-08-23-0101-a
Huanhuan Li, Shukun Yu, Xiaofeng Tang, Yongsheng Liu, Ming Miao
Diaporthe spp. are a significant plant pathogen causing wood canker, blight, dieback, and fruit decay in numerous economically important plant hosts worldwide. D. nobilis has been identified as a highly pathogenic isolate responsible for causing kiwifruit (Actinidia sp.) rot, representing one of the most significant threats to the kiwifruit industry. Here, a comprehensive genome-wide sequence of D. nobilis strain DJY16A 5-1 utilizing advanced Nanopore third-generation sequencing technology was present. The genome of D. nobilis strain DJY16A 5-1 was assembled into 26 contigs containing a combined size of 59.28 Mb and N50 length of 4.47 Mb. The virulence-related genes were analyzed, including 3,407 transmembrane proteins, 1,410 secreted proteins, 1,866 signal peptides, 135 effector proteins, 1,069 carbohydrate-active enzymes, 143 membrane transporter proteins, 4,995 pathogen-host interactions related proteins. The genome assembly and annotation facilitate the analysis of pathogen-host interaction, laying the foundation for in-depth research on the infection mechanism of pathogens.
Diaporthe spp.是一种重要的植物病原菌,可导致全球许多具有重要经济价值的植物寄主的木材腐烂、枯萎、坏死和果实腐烂。D. nobilis已被确定为一种高致病性分离株,可导致猕猴桃(Actinidia sp.)腐烂,是猕猴桃产业面临的最大威胁之一。本文利用先进的 Nanopore 第三代测序技术对 D. nobilis 菌株 DJY16A 5-1 进行了全面的全基因组测序。D. nobilis 菌株 DJY16A 5-1 的基因组被组装成 26 个等位组,总大小为 59.28 Mb,N50 长度为 4.47 Mb。分析了与毒力相关的基因,包括 3,407 个跨膜蛋白、1,410 个分泌蛋白、1,866 个信号肽、135 个效应蛋白、1,069 个碳水化合物活性酶、143 个膜转运蛋白、4,995 个病原体-宿主相互作用相关蛋白。基因组的组装和注释为分析病原体与宿主的相互作用提供了便利,为深入研究病原体的感染机制奠定了基础。
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引用次数: 0
Information transfer among grape producers in the western United States on pest and disease management 美国西部葡萄生产者之间的病虫害管理信息传递
Pub Date : 2023-11-15 DOI: 10.1094/phytofr-07-23-0081-r
Sarah R. Lowder, Michelle M. Moyer, Monica L. Cooper, Jay Pscheidt, Walter F. Mahaffee
Knowledge about how producers subjectively assess and communicate about different information resources can help optimize Agricultural Extension efforts. In particular, how do growers use different information resources when making decisions on pest and disease management? Using pest and disease management in wine grapes (Vitis vinifera) as a case study, three surveys were conducted among grape producers in the western US to qualitatively explore resource options (n=15), examine the relative importance of the 23 different information resources identified (n=63), and investigate the social networks where information is passed within and between regions (n=65). Five different informational archetypes emerged, demonstrating different preferences for information resource use which explained 66% of the variance in survey responses. Personal connections (e.g., discussion with professional network, with field foreman and supervisors, and with an Extension agent) were extremely important to the participants. In the communication network analysis, 65 participants were used to form a 324-actor network with 448 links which were then subdivided into intra-state networks. The networks show evidence of structures that facilitate information diffusion and cooperation between independent producers. Additionally, even with networks much smaller than the grape producer populations in these states, influential individuals could be identified. These individuals, when targeted by outreach professionals, could assist with information dissemination, and facilitate changes in opinion or behaviors in the region.
了解生产者如何主观评估和交流不同的信息资源,有助于优化农业推广工作。特别是,种植者在做出病虫害管理决策时如何使用不同的信息资源?我们以酿酒葡萄(Vitis vinifera)的病虫害管理为案例,对美国西部的葡萄生产者进行了三次调查,定性地探讨了资源选择(人数=15),研究了已确定的 23 种不同信息资源的相对重要性(人数=63),并调查了区域内和区域间信息传递的社会网络(人数=65)。调查中出现了五种不同的信息原型,展示了信息资源使用的不同偏好,解释了调查答复中 66% 的差异。个人联系(例如,与专业网络、田间工头和主管以及推广人员进行讨论)对参与者极为重要。在传播网络分析中,65 名参与者组成了一个 324 人的网络,其中有 448 个链接,然后再细分为州内网络。这些网络显示出促进信息传播和独立生产者之间合作的结构。此外,即使网络规模远小于这些州的葡萄生产者人数,也能识别出有影响力的个人。当专业推广人员锁定这些人时,他们可以协助信息传播,并促进该地区舆论或行为的改变。
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