Guevara-Rivera Enrique A, Rodríguez-Negrete Edgar A, Aréchiga-Carvajal Elva T, Leyva-López Norma E, Méndez-Lozano Jesús
Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico.
Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología-Unidad de Manipulación Genética, San Nicolás de los Garza, Mexico.
Front Microbiol. 2022 Apr 25;13:843035. doi: 10.3389/fmicb.2022.843035. eCollection 2022.
Begomoviruses (Family ) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases. High-throughput sequencing (HTS) has provided a powerful tool for speeding up the understanding of molecular ecology and epidemiology of plant virome and for discovery of new viral species. In this study, by performing earlier metagenomics library data mining, followed by geminivirus-related signature single plant searching and RCA-based full-length viral genome cloning, and based on phylogenetic analysis, genomes of two isolates of a novel monopartite begomovirus species tentatively named (GLDV), which infects non-cultivated endemic plant , were identified in Colima, Mexico. Analysis of the genetic structure of both isolates (GLDV-1 and GLDV-2) revealed that the GLDV genome displays a DNA-A-like structure shared with the new world (NW) bipartite begomoviruses. Nonetheless, phylogenetic analysis using representative members of the main begomovirus American clades for tree construction grouped both GLDV isolates in a clade of the monopartite NW begomovirus, (ToLDeV). A comparative analysis of viral replication regulatory elements showed that the GLDV-1 isolate possesses an array and sequence conservation of iterons typical of NW begomovirus infecting the and families. Interestingly, GLDV-2 showed iteron sequences described only in monopartite begomovirus from OW belonging to a sweepovirus clade that infects plants of the family. In addition, the rep iteron related-domain (IRD) of both isolates display FRVQ or FRIS amino acid sequences corresponding to NW and sweepobegomovirus clades for GMV-1 and GMV-2, respectively. Finally, the lack of the GLDV DNA-B segment (tested by molecular detection and biological assays using GLDV-1/2 infectious clones) confirmed the monopartite nature of GLDV. This is the first time that a monopartite begomovirus is described in Mexican ecosystems, and "" geometagenomics analysis indicates that it is restricted to a specific region. These data revealed additional complexity in monopartite begomovirus genetics and geographic distribution and highlighted the importance of metagenomic approaches in understanding global virome ecology and evolution.
菜豆金色花叶病毒属病毒（双生病毒科）是全球范围内一类主要的新兴植物病毒。目前对菜豆金色花叶病毒属病毒的了解大多局限于作物植物系统。然而，已有研究表明，非栽培植物是病毒进化的重要储存库和传播媒介，病毒进化会导致新病害的出现。高通量测序（HTS）为加速理解植物病毒组的分子生态学和流行病学以及发现新的病毒种类提供了强大工具。在本研究中，通过对早期宏基因组文库数据进行挖掘，随后进行与双生病毒相关的特征单株搜索以及基于滚环扩增（RCA）的全长病毒基因组克隆，并基于系统发育分析，在墨西哥科利马发现了一种新型单分体菜豆金色花叶病毒属病毒的两个分离株的基因组，该病毒暂命名为 （GLDV），可感染非栽培的地方特有植物 。对两个分离株（GLDV - 1和GLDV - 2）的遗传结构分析表明，GLDV基因组呈现出与新大陆（NW）双分体菜豆金色花叶病毒属病毒共有的类DNA - A结构。尽管如此，使用美洲主要菜豆金色花叶病毒属病毒分支的代表性成员构建系统发育树时，两个GLDV分离株被归为单分体NW菜豆金色花叶病毒属病毒 （ToLDeV）的一个分支。对病毒复制调控元件的比较分析表明，GLDV - 1分离株具有一系列典型的NW菜豆金色花叶病毒属病毒感染 科和 科植物的迭代子序列保守性。有趣的是，GLDV - 2显示出仅在属于感染 科植物的帚状病毒属分支的旧大陆（OW）单分体菜豆金色花叶病毒属病毒中描述的迭代子序列。此外，两个分离株的复制相关蛋白迭代子结构域（IRD）分别显示对应于GMV - 1的NW分支和GMV - 2的帚状双生病毒属分支的FRVQ或FRIS氨基酸序列。最后，GLDV缺乏DNA - B片段（通过使用GLDV - 1/2感染性克隆进行分子检测和生物学测定得到证实），这证实了GLDV的单分体性质。这是首次在墨西哥生态系统中描述单分体菜豆金色花叶病毒属病毒，并且“ ”宏基因组分析表明它局限于特定区域。这些数据揭示了单分体菜豆金色花叶病毒属病毒遗传学和地理分布的额外复杂性，并突出了宏基因组方法在理解全球病毒组生态学和进化中的重要性。
