English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Weeds are a source of new viruses but are often neglected during diversity studies. Eleven weed samples previously were collected along the edges of tomato crops in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the southeast of Valle del Cauca. These samples were positive for begomoviruses, but their molecular characterization had not been done until now. For each sample, DNA fragments were cloned, sequenced and analyzed. Nucleotide sequence analysis of viral fragments showed the presence of six different begomoviruses: two viruses isolated from Lantana camara, Desmodium sp. and Amaranthus dubius, which were previously identified as potato yellow mosaic virus (PYMV) and passionfruit leaf distortion virus (PLDV), respectively; four viruses isolated from L. camara, A. dubius, Rivina humilis, Desmodium sp., Rhynchosia minima, Hybanthus attenuatus, Verbena sp., Croton hirtus and Caesalpinia sp., showed the highest nucleotide sequence identity (89%) with the bean chlorotic mosaic virus (BChMV), datura leaf distortion virus (DaLDV) and rhynchosia golden mosaic Yucatan virus (RhGMYV). The cloned virus fragments isolated from these weeds could be new begomoviruses which have not been previously reported before, according with the ICTV species demarcation criteria established for the Begomovirus genera (≥91 % sequence identity). In this study, mixed infections of begomoviruses were founded in Desmodium sp. and A. dubius. Finally, this paper reports for the first time the identification of three alternative begomovirus weeds: A. dubius for PYMV and L. camara and Desmodium sp. for PLDV, both viruses which infect tomato and passion fruit crops, respectively. Additional key words: geminivirus; hosts; solanaceae; weed. 1 Universidad Nacional de Colombia, Facultad de Ciencias Agropecuarias, Grupo IPMA Interacción Planta Microorganismo Ambiente, Palmira (Colombia). ORCID Vaca-Vaca J.C.: 0000-0002-8984-540X; ORCID Jara-Tejada F.: 0000-0003-2794-3845; ORCID López-López K.: 0000-0003-3623-4725 2 Corresponding author. klopezl@unal.edu.co The Geminiviridae family is characterized by the presence of single-stranded, circular DNA genomes that are encapsidated in twinned isometric particles of about 18x30 nn. This family is classified into nine genera based on genome organization, vector transmission and host range: Curtovirus, Mastrevirus, Topocuvirus, Becurtovirus, Eragrovirus, Turncurtovirus, Capulavirus, Grablovirus and Begomovirus (Zerbini et al., 2017). The begomovirus genomes endemic to the Western Hemisphere (>322 species) consist of DNAA and DNA-B components, each of 2.5-2.6 kb, are transmitted by members of a whitefly cryptic species complex [Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae)], and cause economically important diseases in most tropical and subtropical regions of the world (Brown et al., 2015; Gilbertson et al., 2016). Many scientific reports suggest that weeds are potential sources of primary inoculum and play an important role as reservoirs and alternative hosts that spread viruses to new host crops and lead to major yield losses (Barreto et al., 2013; Prajapat et al., 2014; Vaca-Vaca et al., 2018). Therefore, the epidemiology of the geminivirus is incomplete without the study of weeds with crop-infecting begomoviruses that may have arisen from endemic weed-infecting viruses; there are known weed-infecting begomoviruses that can infect crops (Sanchez-Campos et al., 2000; Andrade et al., 2006). Wild hosts, such as weeds, are sites where begomoviruses carry out processes of genetic recombination or pseudo-recombination, decisive steps in the evolution of viruses. In addition to the processes of competition and selection, they can generate new variants of viruses with attenuated or higher pathogenicity in a short period of time (Padidam et al., 1999; Da Silva et al., 2011). Studies on viruses are of special importance to finding virus control measures in crops (Gallo et al., 2018). Research on bipartite begomoviruses in Colombia is still very limited. Right now in Colombia, there are five reported virus species: bean dwarf mosaic virus (BDMV) (Gilbertson et al., 1991), bean leaf crumple virus (BLCrV) (Carvajal-Yepes et al., 2017), potato yellow mosaic virus (PYMV) (Martínez et al., 2008; Vaca-Vaca et al., 2012), and passionfruit leaf distortion virus (PDLV) (Vaca-Vaca et al., 2017), which have been isolated from beans, tomato and passion fruit ResUmen Las arvenses son una fuente de nuevos virus, pero a menudo se descuidan durante los estudios de diversidad. Previamente, se recolectaron once muestras de arvenses a lo largo de los bordes de un campo de cultivo de tomate ubicado en cuatro municipios (Florida, Ginebra, Cerrito y Candelaria) en el sureste del Valle del Cauca. Estas muestras fueron positivas para begomovirus, pero su caracterización molecular no se había realizado hasta ahora. Para cada muestra, se clonaron, secuenciaron y analizaron fragmentos de DNA. El análisis de la secuencia de nucleótidos de los fragmentos virales mostró la presencia de seis begomovirus diferentes: dos virus aislados de L. camara, Desmodium sp. y A. dubius fueron descritos previamente como el virus del mosaico amarillo de la papa (PYMV) y el virus de distorsión de la hoja de maracuyá (PLDV), respectivamente; otros cuatro virus que se aislaron de L. camara, A. dubius, R. humilis, Desmodium sp., R. minima, H. attenuatus, Verbena sp., C. hirtus y Caesalpinia sp., mostraron su mayor identidad de secuencia de nucleótidos (89%) con el virus del mosaico clorótico del frijol (BChMV), el virus de la distorsión de la hoja de la datura (DaLDV) y el virus del mosaico dorado de rhynchosia de Yucatán (RhGMYV). Los fragmentos de virus clonados de estas malezas podrían ser begomovirus nuevos que no se reportaron anteriormente, esto de acuerdo con el criterio de demarcación de especies de ICTV para el género Begomovirus (≥ 91% de identidad de secuencia). Este análisis también encontró la presencia de infecciones mixtas de begomovirus en las arvenses Desmodium sp. y A. dubius. Finalmente, este artículo reporta por primera vez tres arvenses hospederas alternativas de begomovirus que infectan cultivos de tomate y maracuyá: A. dubius para PYMV, y L. camara y Desmodium sp. para PLDV, respectivamente. Palabras clave adicionales: geminivirus; hospederos; solanaceae; arvense. Received for publication: 09-12-2019 accepted for publication: 30-03-2020 INTRODUCTION 116 vaca-vaca / JaRa-teJada / lóPeZ-lóPeZ Rev. Colomb. Cienc. Hortic. crops, respectively. Recently, a new begomovirus was detected in chili peppers (Capsicum spp.) in Valle del Cauca but its identity is being studied (Vaca-Vaca et al., 2019b). In addition, begomoviruses detection has been done in weeds collected from tomato crops in Valle del Cauca, such as Rivina humilis, Lapoerta aestuans, Lantana camara, Amaranthus dubius, Desmodium sp., Momordica charantia, Hybanthus attenuates, Verbena sp., Croton hirtus, Rhynchosia minima and Caesalpinia sp. (López-López et al., 2012; 2014). In 2018 and 2019, the complete genomes of begomoviruses were found in C. hirtus and R. minima, both new begomoviruses with the proposed names Croton golden mosaic virus (CroGMV) and Rhynchosia golden mosaic Colombia virus (RhGMCV), respectively. (Vaca-Vaca et al., 2018; López-López et al., 2019). Recently, new begomovirus hosts were identified in a study conducted in Valle del Cauca on weeds associated with chili pepper crops: Parthenium hysterophorus, Malvastrum sp., Sida acuta, Acalypha sp., Euphorbia hirta, R. minima and R. humilis (Vaca-Vaca et al., 2019a). The increasing occurrence of begomoviruses in Colombia demands efforts to study their diversity in order to anticipate and monitor outbreaks, as well as to understand the evolutionary forces driving the emergence of novel begomoviruses in crop species previously reported as unaffected by these pathogens. Previously, a weed survey was conducted by the IPMA research group in tomato crops infected with PYMV in Valle del Cauca, where L. camara, A. dubius, R. humilis, Desmodium sp., R. minima, H. attenuatus, Verbena sp., C. hirtus and Caesalpinia sp. were identified as begomovirus hosts, but the identity of these viruses is still unknown to date (López-López et al., 2014). Therefore, the aim of this research was to characterize begomoviruses present in the weeds samples collected in 2014 along the edges of a tomato crop field located in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the Southeast of Valle del Cauca. The information obtained in this research could be useful for designing future effective strategies for the control of geminiviral diseases in crops. MATERIALS AND METHODS Sample collection: Weed samples were collected in tomato crops located in the southeast of Valle del Cauca (Colombia), and begomoviruses were detected with PCR (López-López et al., 2014). Eleven begomovirus positive weed samples were used in this research: four weed samples (leaves) were collected in the municipality of Florida: H. attenuates (AT18), Verbena sp. (AT19), C. hirtus (AT20) and L. camara (AT29); one sample was collected in the municipality of Ginebra: A. dubius (AT32); another five weeds were collected in the municipality of Cerrito: R. minima (two samples AT35 and AT36), R. humilis (AT38), Desmodium sp. (AT40) and Caesalpinia sp. (AT41); and the last sample was collected in the municipality of Candelaria: R. humilis (AT61). Amplification and cloning of partial DNA-A component: Plant total DNA was extracted from leaf samples using the Dneasy Plant mini kit (Qiagen®). A 1.2 kb fragment was amplified with PCR with universal primers for members of the Begomovirus genus (Rojas et al., 1992). This fragment spans the 5 ́ region of AC1 (Rep) and coat protein (AR1) genes, and the intergenic region (IR) of the begomovirus. For each sample, a 1.2 kb fragment was cloned in pGEM T-Easy Vector (Promega®) and transformed in E. coli One Shot® (Invit

Partial molecular characterization of begomoviruses isolated from weeds collected in tomato crops in the southeast of Valle del Cauca, Colombia