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学者姓名：高芳銮
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Abstract ：
Advancements in high-throughput sequencing and associated bioinformatics methods have significantly expanded the RNA virus repertoire, including novel viruses with highly divergent genomes encoding "orphan" proteins that apparently lack homologous sequences. This absence of homologs in routine sequence similarity search complicates their taxonomic classification and raises a fundamental question: Do these orphan viral genomes represent bona ide viruses? In 2022, an orphan viral genome encoding a large polyprotein was identified in alfalfa (Medicago sativa) and thrips (Frankliniella occidentalis), and named Snake River alfalfa virus (SRAV). SRAV was initially proposed as an uncommon flavi-like virus identified in a plant host distantly related to family Flaviviridae. Subsequently, another research group showed its common occurrence in alfalfa but challenged its taxonomic position, suggesting it belongs to the family Endornaviridae. In this study, a large-scale analysis of 77 publicly available small RNA datasets indicates that SRAV could be detected across various tissues and cultivars of alfalfa, and has a broad geographical distribution. Moreover, profiles of the SRAV-derived small interfering RNAs (vsiRNAs) exhibited typical characteristics of viruses in plant hosts. The evolutionary analysis suggests that SRAV represents a unique class of plant-hosted flavi-like viruses with an unusual genome organization and evolutionary status, distinct from previously identified flavi-like viruses documented to infect plants. The latter shows a close evolutionary relationship to flavi-like viruses primarily found in plant-feeding invertebrates and lacks evidence of triggering host RNA interference (RNAi) responses so far. Moreover, mining the transcriptome shotgun assembly (TSA) database identified two novel viral sequences with a similar genome organization and evolutionary status to SRAV. In summary, our study resolves the disagreement regarding the taxonomic status of SRAV and suggests the potential existence of two distinct clades of plant-hosted flavi-like viruses with independent evolutionary origins. Furthermore, our research provides the first evidence of plant-hosted flavi-like viruses triggering the host's RNAi antiviral response. The widespread occurrence of SRAV underscores its potential ecological significance in alfalfa, a crop of substantial economic importance.
Keyword ：
endornaviridae endornaviridae flavi-like virus flavi-like virus flaviviridae flaviviridae Snake River Alfalfa virus Snake River Alfalfa virus
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| GB/T 7714 | Xu, Zhongtian , Zheng, Luping , Gao, Fangluan et al. An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants [J]. | VIRUS EVOLUTION , 2025 , 11 (1) . |
| MLA | Xu, Zhongtian et al. "An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants" . | VIRUS EVOLUTION 11 . 1 (2025) . |
| APA | Xu, Zhongtian , Zheng, Luping , Gao, Fangluan , Li, Yiyuan , Sun, Zongtao , Chen, Jianping et al. An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants . | VIRUS EVOLUTION , 2025 , 11 (1) . |
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Anthracnose, caused by Colletotrichum truncatum, is an economically important disease in soybean plants. Florylpicoxamid, a novel quinone inside inhibitor (QiI) fungicide, exhibits broad spectrum activity against pathogenic ascomycete fungi. However, little is known about the development of resistance risk to florylpicoxamid and the underlying mechanisms in C. truncatum. In the current study, the sensitivities of C. truncatum isolates to florylpicoxamid were characterized, with an average EC50 value of 0.1540 +/- 0.1642 mu g/mL. Eleven florylpicoxamid-resistant mutants were obtained, which exhibited fitness comparable to that of the parental isolates. Florylpicoxamid treatment had a lesser impact on ATP production and the activity of the cytochrome bc1 complex in the mutants compared to the parental isolates. Overall, C. truncatum has a medium resistance risk to florylpicoxamid. Additionally, cross-resistance was not observed between florylpicoxamid and the other fungicides tested herein. Three types of point mutations in the Cyt b protein, N31S/A37V, A37V, and S207P, were found to confer varying levels of resistance to florylpicoxamid in C. truncatum, as further proved by molecular docking.
Keyword ：
Colletotrichum truncatum Colletotrichum truncatum cytochrome b cytochrome b florylpicoxamid florylpicoxamid molecular docking molecular docking resistance mutation resistance mutation
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| GB/T 7714 | Shi, Niuniu , Zou, Huajiao , Qiu, Dezhu et al. Resistance Risk and Novel Resistance-Related Point Mutations in Target Protein Cyt b of Florylpicoxamid in Colletotrichum truncatum [J]. | JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY , 2025 , 73 (9) : 5289-5299 . |
| MLA | Shi, Niuniu et al. "Resistance Risk and Novel Resistance-Related Point Mutations in Target Protein Cyt b of Florylpicoxamid in Colletotrichum truncatum" . | JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 73 . 9 (2025) : 5289-5299 . |
| APA | Shi, Niuniu , Zou, Huajiao , Qiu, Dezhu , Chen, Furu , Gao, Fangluan , Du, Yixin . Resistance Risk and Novel Resistance-Related Point Mutations in Target Protein Cyt b of Florylpicoxamid in Colletotrichum truncatum . | JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY , 2025 , 73 (9) , 5289-5299 . |
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<正>槟榔（Areca catechu L.）黄化病（yellow leaf disease, YLD）于1914年首次在印度报道，1981年在海南省屯昌县发现
Keyword ：
areca palm latent totivirus areca palm latent totivirus ORFan ORFan RNA-dependent RNA polymerase RNA-dependent RNA polymerase Totivirus Totivirus
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| GB/T 7714 | 肖思云 , 牛晓庆 , 徐钟天 et al. 海南槟榔潜隐单组分病毒1的分子进化特征分析 [J]. | 植物病理学报 , 2025 , 55 (03) : 550-554 . |
| MLA | 肖思云 et al. "海南槟榔潜隐单组分病毒1的分子进化特征分析" . | 植物病理学报 55 . 03 (2025) : 550-554 . |
| APA | 肖思云 , 牛晓庆 , 徐钟天 , 田雨菁 , 谢源 , 杜振国 et al. 海南槟榔潜隐单组分病毒1的分子进化特征分析 . | 植物病理学报 , 2025 , 55 (03) , 550-554 . |
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Areca palm velarivirus 1 (APV1), the causal agent of yellow leaf disease (YLD), poses a serious threat to the economically important areca palm industry in the Hainan Province, China, yet its evolutionary dynamics remain poorly understood. Here, we performed a large-scale molecular survey by sequencing the coat protein (CP) gene from 364 APV1-infected samples collected across major cultivation regions of Hainan. Population genetic analyses revealed extremely high haplotype diversity (Hd = 0.997) but very low nucleotide diversity (pi = 0.017). Neutrality tests (Tajima's D = -2.266; Fu's FS = -23.697) and a unimodal mismatch distribution supported a scenario of recent demographic expansion from a restricted ancestral pool. Evolutionary analyses indicated that the CP gene is subject to strong purifying selection, although eight codons exhibited episodic positive selection, suggesting ongoing viral adaptation. Furthermore, we identified three distinct genetic clusters with significant geographic structuring, indicating that viral dissemination is shaped by local factors. Together, these results reveal a recent explosive invasion of APV1 characterized by rapid island-wide expansion and emerging local differentiation. This work provides novel insights into the evolutionary trajectory of APV1 and establishes a genomic basis for improved surveillance and management of YLD.
Keyword ：
areca palm areca palm areca palm velarivirus 1 areca palm velarivirus 1 demographic expansion demographic expansion genetic diversity genetic diversity natural selection natural selection population structure population structure
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| GB/T 7714 | Niu, Xiaoqing , Xu, Zhongtian , Lin, Zhaowei et al. Population Genetic Analysis Reveals Recent Demographic Expansion and Local Differentiation of Areca Palm Velarivirus 1 in Hainan Island [J]. | PLANTS-BASEL , 2025 , 14 (19) . |
| MLA | Niu, Xiaoqing et al. "Population Genetic Analysis Reveals Recent Demographic Expansion and Local Differentiation of Areca Palm Velarivirus 1 in Hainan Island" . | PLANTS-BASEL 14 . 19 (2025) . |
| APA | Niu, Xiaoqing , Xu, Zhongtian , Lin, Zhaowei , Tang, Qinghua , Du, Zhenguo , Gao, Fangluan . Population Genetic Analysis Reveals Recent Demographic Expansion and Local Differentiation of Areca Palm Velarivirus 1 in Hainan Island . | PLANTS-BASEL , 2025 , 14 (19) . |
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BACKGROUND Colletotrichum scovillei is a major fungal pathogen responsible for anthracnose disease, posing a growing threat to global chili production. Mefentrifluconazole, a novel isopropanol-triazole fungicide, exhibits strong efficacy against a broad spectrum of plant pathogens. However, the resistance risk of mefentrifluconazole in Colletotrichum scovillei and the associated molecular mechanisms remain poorly characterized.RESULTS In this study, we evaluated the sensitivity of 102 Colletotrichum scovillei isolates to mefentrifluconazole, revealing a half-maximal effective concentration (EC50) value of 0.6924 +/- 0.1482 mu g mL-1. Through fungicide adaptation, seven stable resistant mutants were generated from four sensitive parental isolates, with resistance factors ranging from 3.73 to 26.51. Compared to their parental isolates, the resistant mutants displayed similar or reduced fitness in terms of growth, sporulation and pathogenicity. Cross-resistance assays indicated that mefentrifluconazole exhibited positive cross-resistance with difenoconazole, propiconazole and prochloraz, but not with pyraclostrobin, florylpicoxamid or fluazinam. Further biochemical analysis demonstrated that mefentrifluconazole treatment resulted in a significantly higher inhibition rate of ergosterol biosynthesis in parental isolates relative to resistant mutants. A similar finding was observed in cell membrane damage assessment. Molecular investigations revealed no mutations in CYP51 paralogs among resistant mutants; however, quantitative analysis confirmed the overexpression of CYP51 paralogs in these isolates following mefentrifluconazole exposure.CONCLUSION Together, there is a low risk of Colletotrichum scovillei developing resistance to mefentrifluconazole, and the induced overexpression of CYP51 paralogs may contribute to potential mefentrifluconazole resistance in this pathogen. These findings offer significant implications for formulating effective management strategies against anthracnose. (c) 2025 Society of Chemical Industry.
Keyword ：
Colletotrichum scovillei Colletotrichum scovillei fungicide resistance fungicide resistance mefentrifluconazole mefentrifluconazole overexpression overexpression resistance mechanism resistance mechanism
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| GB/T 7714 | Shi, Niuniu , Wang, Qinghai , He, Jingyi et al. Unveiling the resistance risk and mechanism of mefentrifluconazole in Colletotrichum scovillei [J]. | PEST MANAGEMENT SCIENCE , 2025 . |
| MLA | Shi, Niuniu et al. "Unveiling the resistance risk and mechanism of mefentrifluconazole in Colletotrichum scovillei" . | PEST MANAGEMENT SCIENCE (2025) . |
| APA | Shi, Niuniu , Wang, Qinghai , He, Jingyi , Zheng, Xuefang , Du, Yixin , Gao, Fangluan . Unveiling the resistance risk and mechanism of mefentrifluconazole in Colletotrichum scovillei . | PEST MANAGEMENT SCIENCE , 2025 . |
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【目的】以柑橘硼毒害响应关键基因MIR397为切入点筛选上游调控因子，以期为柑橘响应硼毒害的分子网络研究和定向品种改良提供理论参考。【方法】以雪柑（Citrus sinensis）和酸柚（C. grandis）为材料，采用SMART技术构建硼毒害处理叶片的均一化酵母单杂交三框cDNA文库，以硼毒害响应关键基因MIR397启动子中的脱落酸响应元件（Abscisic Acid Response Element, ABRE）、胚乳发育元件（General Control Non-repressed Protein 4,GCN4）、 BoxII-like元件（BoxII-likeCis-actingElement,BoxII-like）和乙烯响应元件（EthyleneResponseElement,ERE）为诱饵筛选上游的调控因子。【结果】所建三框文库容量分别为1.5×106、1.5×106、1.6×106 CFU，外源基因插入片段长度为500～4 000 bp，重组率为100%，初级文库96克隆测序冗余率为0%;cDNA三框表达文库滴度4×109 CFU·mL-1，满足酵母单杂交cDNA文库构建要求。单杂交文库筛选结果获得23条表达序列标签（expressed sequence tag, EST），其中ABRE元件11条、GCN4元件3条、ERE元件9条；60.87%的EST序列与植物的生长发育、逆境响应、信号转导及转录调控相关，17.39%的EST与蛋白质翻译相关，其余被注释的EST为蛋白酶。Y1H点对点验证HAP3、BBX和EIN3与ERE元件存在互作。【结论】本研究通过酵母单杂交文库筛选得到3个与硼毒害响应关键基因MIR397启动子ERE元件存在互作的转录因子，为进一步研究柑橘响应硼毒害的分子网络奠定基础。
Keyword ：
cDNA三框文库 cDNA三框文库 启动子 启动子 柑橘 柑橘 硼毒害 硼毒害 调控因子 调控因子
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| GB/T 7714 | 黄镜浩 , 林雄杰 , 陈木兰 et al. 硼毒害柑橘酵母单杂交文库构建及MIR397上游调控因子筛选 [J]. | 福建农业学报 , 2025 , 40 (03) : 225-233 . |
| MLA | 黄镜浩 et al. "硼毒害柑橘酵母单杂交文库构建及MIR397上游调控因子筛选" . | 福建农业学报 40 . 03 (2025) : 225-233 . |
| APA | 黄镜浩 , 林雄杰 , 陈木兰 , 饶文华 , 和静怡 , 高芳銮 et al. 硼毒害柑橘酵母单杂交文库构建及MIR397上游调控因子筛选 . | 福建农业学报 , 2025 , 40 (03) , 225-233 . |
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Tomato chlorosis virus (ToCV), first reported in Florida, USA, in 1998, has since emerged in multiple regions worldwide, posing a significant threat to global tomato production. However, its origin, migration patterns, and evolutionary history remain poorly understood. In this study, we used Bayesian phylogeographic analysis of coat protein gene sequences from 155 ToCV isolates to reconstruct its phylogeographic history. Our results show that ToCV evolves at a rate of 6.24 x 10-4 subs/site/year (95% credibility interval: 4.35 x 10-4-8.28 x 10-4), with the most recent common ancestor dating back to 1882. The maximum clade credibility (MCC) tree revealed three major clades, with Clade 1-whose most recent common ancestor dates to approximately 1975-comprising over 90% of the isolates. Although the exact origin of ToCV remains uncertain, we identified five distinct migration pathways: one from Europe to the Americas, one from Europe to South Asia, one from the Middle East to East Asia, one from East Asia to mainland China, and one from mainland China to Europe. These findings underscore the complex global spread of ToCV and suggest that multiple geographic areas have contributed to its ongoing evolution and dissemination.
Keyword ：
Bayesian phylodynamics Bayesian phylodynamics tomato chlorosis virus tomato chlorosis virus virus dispersal virus dispersal
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| GB/T 7714 | Wu, Kangcheng , Zhang, Shiwei , Huang, Wende et al. Phylogeographic History of Tomato Chlorosis Virus [J]. | VIRUSES-BASEL , 2025 , 17 (4) . |
| MLA | Wu, Kangcheng et al. "Phylogeographic History of Tomato Chlorosis Virus" . | VIRUSES-BASEL 17 . 4 (2025) . |
| APA | Wu, Kangcheng , Zhang, Shiwei , Huang, Wende , Du, Zhenguo , Gao, Fangluan , Guan, Xiayu . Phylogeographic History of Tomato Chlorosis Virus . | VIRUSES-BASEL , 2025 , 17 (4) . |
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Maize, a staple food and cash crop worldwide, also serves as a critical industrial raw material. However, it is significantly threatened by viral pathogens, particularly maize dwarf mosaic virus (MDMV), the primary cause of maize dwarf mosaic disease, a debilitating condition affecting maize cultivation. This study aims to establish a multi-gene combined RT-PCR assay for the rapid specific, sensitive, and reliable detection of MDMV without the need for special expensive equipment. Samples of imported maize, sorghum, and barley were collected from ports in Fujian and Shanghai. Primers targeting the coat protein (CP) and cytoplasmic inclusion protein (CI) genes of MDMV were designed and optimized. Through the design and screening of primers, as well as the optimization of reaction conditions and primer concentrations, a multi-gene combined RT-PCR assay was established to simultaneously detect both genes. Additionally, a real-time fluorescent-based RT-PCR (RT-qPCR) assay was developed using the CP gene to confirm the accuracy of multi-gene combined RT-PCR assay. The sensitivity of the optimized multi-gene combined RT-PCR assay enables the detection of MDMV in infected maize leaf crude extracts at dilutions of 5.37 pg/mu L. This assay exhibited excellent specificity, high sensitivity, and robust repeatability, providing swift and accurate detection of MDMV. The multi-gene combined RT-PCR assay offers precise and efficient technical support for MDMV detection and contributes to improved maize production practices.
Keyword ：
maize dwarf mosaic virus maize dwarf mosaic virus molecular detection molecular detection multi-gene combined RT-PCR assay multi-gene combined RT-PCR assay real-time quantitative PCR detection (RT-qPCR) real-time quantitative PCR detection (RT-qPCR)
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| GB/T 7714 | Jin, Yujie , Chen, Xihong , Li, Min et al. A Novel Multi-Gene Combined RT-PCR Assay for Rapid and Sensitive Detection of Maize Dwarf Mosaic Virus [J]. | VIRUSES-BASEL , 2025 , 17 (3) . |
| MLA | Jin, Yujie et al. "A Novel Multi-Gene Combined RT-PCR Assay for Rapid and Sensitive Detection of Maize Dwarf Mosaic Virus" . | VIRUSES-BASEL 17 . 3 (2025) . |
| APA | Jin, Yujie , Chen, Xihong , Li, Min , Zhang, Xiaoqi , Cai, Wei , Shen, Jianguo et al. A Novel Multi-Gene Combined RT-PCR Assay for Rapid and Sensitive Detection of Maize Dwarf Mosaic Virus . | VIRUSES-BASEL , 2025 , 17 (3) . |
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MCMCtree and r8s are among the most popular molecular dating tools in the current genomic era, but their utility is hampered by steep learning curves, particularly concerning input file formatting, the complexity of fossil calibration setup, tree visualization, and model selection. To enhance their usability and improve research efficiency, we developed three new tools: MDGUI (for molecular dating analysis), TimeTreeAnno (for timetree visualization), and MCMCTracer (for convergence assessment). We integrated these into the PhyloSuite v2 platform, along with MCMCtree and r8s plugins, to create a comprehensive molecular dating suite. Compared to existing solutions that we benchmarked, our toolkit offers a more intuitive interface and streamlined workflow, featuring visual calibration point configuration, support for multiple alignment formats, automated model selection and implementation for downstream analyses, one-click pause/resume functionality, multithreading acceleration, and on-demand MCMC convergence assessment and plotting. Furthermore, PhyloSuite v2 introduces other advanced features, including gene duplicate resolution during the extraction step, significantly accelerated data handling capabilities (specifically, format conversion and concatenation), deeper integration of the latest IQ-TREE models and functions, and further streamlining of the entire phylogenetic analysis workflow. The update also includes adaptation to high-resolution screens and numerous bug fixes. The source code for the new version of PhyloSuite is available at https://github.com/dongzhang0725/PhyloSuite.
Keyword ：
annotation annotation graphical user interface graphical user interface MCMCtree MCMCtree molecular dating molecular dating phylogenetic analysis phylogenetic analysis r8s r8s visualization visualization
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| GB/T 7714 | Zhao, Dong , Ye, Tong , Gao, Fangluan et al. PhyloSuite v2: The development of an all-in-one, efficient and visualization-oriented suite for molecular dating analysis and other advanced features [J]. | IMETA , 2025 . |
| MLA | Zhao, Dong et al. "PhyloSuite v2: The development of an all-in-one, efficient and visualization-oriented suite for molecular dating analysis and other advanced features" . | IMETA (2025) . |
| APA | Zhao, Dong , Ye, Tong , Gao, Fangluan , Jakovlic, Ivan , La, Qiong , Tong, Yindong et al. PhyloSuite v2: The development of an all-in-one, efficient and visualization-oriented suite for molecular dating analysis and other advanced features . | IMETA , 2025 . |
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建兰花叶病毒（Cymbidium mosaic virus,CymMV）是危害兰花并造成重要经济损失的病毒之一。为揭示CymMV的遗传变异及其适应性进化特征，新测定了16个CymMV石斛兰（Dendrobium nobile）分离物的外壳蛋白基因（coat protein,CP）序列，并结合已报道的52个CymMV中国分离物CP基因序列进行遗传变异及进化分析。遗传多样性分析结果显示，68个CymMV分离物CP基因的核苷酸多样性（P_i）和单倍型多样性（Hd）平均值分别为0.039和0.992，表明该病毒具有较高的遗传多样性。分子变异分析（analysis of molecular variance,AMOVA）显示，CymMV变异源主要来自于病毒个体，约占总变异的71.72%。群体遗传结构分析显示，该病毒可以分为两个大簇（Cluster）,CymMV建兰（Cymbidium ensifolium）分离物独立为一簇（Cluster 1），其他寄主分离物聚为另一大簇（Cluster 2）,Cluster2内相同寄主来源的病毒分离物倾向于相聚成簇。进一步的系统发育与性状关联分析结果显示CymMV与寄主来源存在显著的关联性。上述结果表明，CymMV的遗传变异具有寄主特异性，其适应性进化主要受寄主因素所驱动。
Keyword ：
主成分判别分析 主成分判别分析 外壳蛋白基因 外壳蛋白基因 建兰花叶病毒 建兰花叶病毒 适应性进化 适应性进化 遗传多样性 遗传多样性
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| GB/T 7714 | 关夏玉 , 陈细红 , 郭菁 et al. 建兰花叶病毒的遗传变异及其寄主适应性 [J]. | 园艺学报 , 2024 , 51 (01) : 203-212 . |
| MLA | 关夏玉 et al. "建兰花叶病毒的遗传变异及其寄主适应性" . | 园艺学报 51 . 01 (2024) : 203-212 . |
| APA | 关夏玉 , 陈细红 , 郭菁 , 吕浩阳 , 梁晨媛 , 高芳銮 . 建兰花叶病毒的遗传变异及其寄主适应性 . | 园艺学报 , 2024 , 51 (01) , 203-212 . |
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