Roy Avijit, Shao Jonathan, Espindola Andres S, Ramos Lopez Daniel, Otero-Colina Gabriel, Rivera Yazmín, Mavrodieva Vessela A, Nakhla Mark K, Schneider William L, Cardwell Kitty
Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center (BARC), United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Beltsville, MD 20705, USA.
Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center (BARC), United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Beltsville, MD 20705, USA.
Viruses. 2025 Mar 19;17(3):441. doi: 10.3390/v17030441.
is a recently accepted plant virus genus within the family . Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by spp. Currently, there are five recognized species and two unclassified members in the genus Four out of seven-orchid fleck virus (OFV), citrus leprosis virus N, citrus chlorotic spot virus, and citrus bright spot virus-can infect citrus and produce leprosis disease-like symptoms. The E-probe Diagnostic for Nucleic Acid Analysis (EDNA) was developed to reduce computational effort and then integrated within Microbe-Finder (MiFi) online platform to design and evaluate e-probes in raw High Throughput Sequencing (HTS) data. During this study, genomes were downloaded from public databases and e-probes were designed using the MiProbe incorporated into the MiFi platform. Three different sizes of e-probes, 40, 60, and 80 nucleotides, were developed and selected based on whole genome comparisons with near-neighbor genomes. For curation, each e-probe was searched in the NCBI nucleotide sequence database using BLASTn. All the e-probes that had hits with non-target species with ≥90% identities were removed. The sensitivity and specificity of genus, species, strain, and variant-specific e-probes were validated in vivo using HTS meta-transcriptomic libraries generated from -suspected citrus, orchid, and ornamentals. Through downstream analysis of HTS data, EDNA not only detected the known hosts of OFV but also discovered an unknown host leopard plant (), and the possible existence of a new ornamental strain of OFV in nature.
是该科中最近被认可的一个植物病毒属。归入该属的物种由双节段、负义、单链RNA病毒组成，由 属昆虫传播。目前，该属有五个公认的物种和两个未分类的成员。七种中的四种——兰花斑点病毒（OFV）、柑橘麻风病病毒N、柑橘褪绿斑点病毒和柑橘亮斑病毒——可感染柑橘并产生类似麻风病的症状。开发了用于核酸分析的E探针诊断法（EDNA）以减少计算量，然后将其整合到微生物发现者（MiFi）在线平台中，用于在原始高通量测序（HTS）数据中设计和评估E探针。在这项研究中，从公共数据库下载了 基因组，并使用MiFi平台中包含的MiProbe设计了E探针。基于与近邻基因组的全基因组比较，开发并选择了三种不同大小的E探针，分别为40、60和80个核苷酸。为了进行筛选，使用BLASTn在NCBI核苷酸序列数据库中搜索每个E探针。所有与非靶标物种有≥90%同一性匹配的E探针都被去除。使用从疑似感染 的柑橘、兰花和观赏植物中生成的HTS宏转录组文库，在体内验证了 属、种、株和变种特异性E探针的敏感性和特异性。通过对HTS数据的下游分析，EDNA不仅检测到了OFV的已知宿主，还发现了一种未知宿主豹纹竹芋（ ），以及自然界中可能存在的一种新的OFV观赏株系。
