Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus-Petunia isolate and its associated betasatellite

Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10-3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined.

DETECCIÓN MOLECULAR DE BEGOMOVIRUS AISLADOS DE ARVENSES ASOCIADAS AL CULTIVO DE AJÍ (Capsicum spp.) EN EL VALLE DEL CAUCA, COLOMBIA

Los virus Potato yellow mosaic virus (PYMV/Co), Passionfruit leaf distortion virus (PLDV), Pepper rugose mosaic virus (PRMV) y Rhynchosia golden mosaic Colombia virus (RhGMCV) son begomovirus de interés agrícola, aislados y caracterizados molecularmente en el Valle del Cauca. Sin embargo, en la actualidad no hay suficiente información sobre sus hospederos alternos. Dado que las arvenses cumplen un papel importante en la ecología y epidemiología viral, este estudio tuvo como objetivo detectar la presencia de estos begomovirus en arvenses asociadas al cultivo de ají en el Valle del Cauca, Colombia. Se recolectaron 121 plantas arvenses en zonas productoras de ají, localizadas en 7 municipios del Valle del Cauca, las cuales fueron identificadas a nivel taxonómico. A partir del ADN genómico purificado de estas plantas se evaluó la presencia de virus por PCR, usando cebadores universales para el género Begomovirus y específicos para PYMV/Co, PLDV, PRMV y RhGMCV. Se detectaron begomovirus en 15 de las especies de arvenses evaluadas. Esta es la primera vez que las especies Ipomoea tiliacea, Melothria pendula, Caperonia palustris, Desmodium tortuosum, Desmodium intortum, Ammannia coccinea, Panicum polygonatum, Capsicum rhomboideum, Eclipta prostrata y Synedrella nodiflora se reportan como hospederas de begomovirus en Colombia. Se detectaron los begomovirus RhGMCV, PYMV/Co, PRMV y PLDV en infecciones simples y mixtas. Estos resultados aportan nuevos datos sobre los hospederos alternos de begomovirus. Esta información servirá para implementar un plan de manejo integrado de enfermedades virales con el potencial para afectar negativamente el rendimiento del cultivo de ají, y otros cultivos en Colombia.

Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications

Simple Summary

Begomovirus has a wide host range and threatens a significant amount of economic damage to many important crops such as tomatoes, beans, cassava, squash and cotton. There are many efforts directed at controlling this disease including the use of insecticides to control the insect vector as well as screening the resistant varieties. The use of synthetic virus or infectious clones approaches has allowed plant virologists to characterize and exploit the genome virus at the molecular and biological levels. By exploiting the DNA of the virus using the infectious clones strategy, the viral genome can be manipulated at specific regions to study functional genes for host–virus interactions. Thus, this review will provide an overview of the strategy to construct infectious clones of Begomovirus. The significance of established infectious clones in Begomovirus study will also be discussed.

Abstract

Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

Interaction of eukaryotic proliferating cell nuclear antigen (PCNA) with the replication-associated protein (Rep) of cotton leaf curl Multan virus and pedilanthus leaf curl virus

The replication-associated (Rep) proteins of pathogenic begomoviruses, including cotton leaf curl Multan virus (CLCuMuV) and pedilanthus leaf curl virus (PeLCV), interact with the DNA replication machinery of their eukaryotic hosts. The analysis of Rep protein sequences showed that there is 13-28% sequence variation among CLCuMuV and PeLCV isolates, with phylogenetic clusters that can separated at least in part based on the country of origin of the respective viruses. To identify specific host factors involved in the virus replication cycle, we conducted yeast two-hybrid assays to detect possible interactions between the CLCuMuV and PeLCV Rep proteins and 30 protein components of the Saccharomyces cerevisiae DNA replication machinery. This showed that the proliferating cell nuclear antigen (PCNA) protein of S. cerevisiae interacts with Rep proteins from both CLCuMuV and PeLCV. We used the yeast PCNA sequence in BLAST comparisons to identify two PCNA orthologs each in Gossypium hirsutum (cotton), Arabidopsis thaliana (Arabidopsis), and Nicotiana benthamiana (tobacco). Sequence comparisons showed 38-40% identity between the yeast and plant PCNA proteins, and > 91% identity among the plant PCNA proteins, which clustered together in one phylogenetic group. The expression of the six plant PCNA proteins in the yeast two-hybrid system confirmed interactions with the CLCuMuV and PeLCV Rep proteins. Our results demonstrate that the interaction of begomovirus Rep proteins with eukaryotic PCNA proteins is strongly conserved, despite significant evolutionary variation in the protein sequences of both of the interacting partners.

Diversity and recombination analysis of Cotton leaf curl Multan virus: a highly emerging begomovirus in northern India

BACKGROUND

Cotton leaf curl disease (CLCuD), caused by begomoviruses in association with satellite molecules, is a major threat to cotton production causing enormous losses to cotton crop in most of the cotton growing countries including Indian subcontinent. In this study, isolates of begomovirus and satellite molecules associated with CLCuD were collected from North India (Haryana, New Delhi). They were amplified employing rolling circle replication mechanism, cloned, sequenced and, their phylogenetic and recombination analysis was performed.

RESULTS

The five Cotton leaf curl Multan virus (CLCuMuV) isolates investigated in this study showed monopartite organization of the genome typical of Old World begomoviruses. Nucleotide sequence analyses assigned them as the strains of CLCuMuV and were designated as CLCuMuV-SR13, CLCuMuV-SR14, CLCuMuV-ND14, CLCuMuV-ND15 and CLCuMuV-SR15. The genome of CLCuMuV-SR13 shared a highest level of nucleotide sequence identity (98%) with CLCuMuV (JN678804), CLCuMuV-SR14 and CLCuMuV-SR15 exhibited 96% with CLCuMuV (KM096471), while isolates CLCuMuV-ND15 and CLCuMuV-SR15 revealed 96% sequence identity with CLCuMuV (AY765253). The four betasatellite molecules investigated in this study shared 95-99% nucleotide sequence identity with Cotton leaf curl Multan betasatellite (CLCuMB) from India. The betasatellite molecules were designated as CLCuMB-SR13, CLCuMB-SR14, CLCuMB-ND14 and CLCuMB-ND15. Alphasatellite molecules in this study, designated as GLCuA-SR14, GLCuA-ND14 and GLCuA-SR15, revealed 98% identity with Guar leaf curl alphasatellite (GLCuA) reported from Pakistan.

CONCLUSION

The phylogenetic and recombination studies concluded that the isolates of CLCuMuV genomes undertaken in this study have a potential recombinant origin. Remarkably, significant recombination was detected in almost all the genes with contribution of Cotton leaf curl Kokhran Virus (CLCuKoV) in IR, V1, V2, C1, C4 and C5 regions and of CLCuMuV in C2 region of CLCuMuV-SR14. CLCuKoV also donated in C2, C3 regions of CLCuMuV-ND14; V1, V2, C2 and C3 regions of CLCuMuV-ND15 and C1 of CLCuMuV-SR15. Altogether, these observations signify the uniqueness in Indian CLCuMuV isolates showing contribution of CLCuKoV in all the genes. An interesting observation was frequent identification of GLCuA in CLCuD leaf samples.