A betasatellite-dependent begomovirus infects ornamental rose: characterization of begomovirus infecting rose in Pakistan

Unveiling Lathyrus aphaca L. as a Newly Identified Host for Begomovirus Infection: A Comprehensive Study

The Begomovirus genus of the family Geminiviridae comprises the largest group of geminiviruses. Begomoviruses are transmitted by the whitefly complex (Bemisia tabaci) and infect dicotyledonous plants in tropical and subtropical regions. The list of begomoviruses is continuously increasing as a result of improvements in the methods for identification, especially from weed plants, which are considered a source of new viruses and reservoirs of economically important viruses but are often neglected during diversity studies. Lathyrus aphaca L. weed plants (yellow-flowered pea) with varicose veins and discoloration of the leaves were found. Amplified genomic DNA through rolling circular amplification was subjected to PCR analysis for the detection of the viral genome and associated DNA-satellites (alphasatellites and betasatellites). A full-length sequence (2.8 kb) of a monopartite begomovirus clone was determined; however, we could not find any associated DNA satellites. The amplified full-length clone of Rose leaf curl virus (RoLCuV) reserved all the characteristics and features of an Old World (OW) monopartite begomovirus. Furthermore, it is the first time it has been reported from a new weed host, yellow-flowered pea. Rolling circle amplification and polymerase chain reaction analysis of associated DNA satellites, alphasatellite, and betasatellite, were frequently accomplished but unable to amplify from the begomovirus-infected samples, indicating the presence of only monopartite Old World begomovirus. It is observed that RoLCuV has the capability to infect different hosts individually without the assistance of any DNA satellite component. Recombination in viruses is also a source of begomovirus infection in different hosts.

Genomic properties of allamanda leaf mottle distortion virus, a new begomovirus from golden trumpet (Allamanda cathartica) in India

Golden trumpet (Allamanda cathartica) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-[IN-Al_K1-12]) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India.

Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification

The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.

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

BACKGROUND

Geminiviruses cause major losses to several economically important crops. Pedilanthus leaf curl virus (PeLCV) is a pathogenic geminivirus that appeared in the last decade and is continuously increasing its host range in Pakistan and India. This study reports the identification and characterization of PeLCV-Petunia from ornamental plants in Pakistan, as well as geographical, phylogenetic, and recombination analysis.

METHODS

Viral genomes and associated satellites were amplified, cloned, and sequenced from Petunia atkinsiana plants showing typical geminivirus infection symptoms. Virus-satellite complex was analyzed for phylogenetic and recombination pattern. Infectious clones of isolated virus and satellite molecules were constructed using a partial dimer strategy. Infectivity analysis of PeLCV alone and in combination with Digera yellow vein betasatellite (DiYVB) was performed by Agrobacterium infiltration of Nicotiana benthamiana and Petunia atkinsiana plants with infectious clones.

RESULTS

PeLCV, in association with DiYVB, was identified as the cause of leaf curl disease on P. atkinsiana plants. Sequence analysis showed that the isolated PeLCV is 96-98% identical to PeLCV from soybean, and DiYVB has 91% identity to a betasatellite identified from rose. Infectivity analysis of PeLCV alone and in combination with DiYVB, performed by Agrobacterium infiltration of infectious clones in N. benthamiana and P. atkinsiana plants, resulted in mild and severe disease symptoms 14 days after infiltration, respectively, demonstrating that these viruses are natural disease-causing agents. Southern blot hybridization indicated successful replication of the virus-betasatellite complex in the infected plants. Phylogenetic analysis suggests that PeLCV originated from Pakistan and later spread to India. Recombination analysis predicted that PeLCV is a donor parent for recombination and evolution of two important begomoviruses, Papaya leaf curl virus (PaLCuV) and Radish leaf curl virus (RaLCuV). The molecular phylogeny of genes encoding coat protein (CP) and replication associated protein (Rep) depict a complex evolutionary pattern of the viruses, with wide diversity in both of the genes.

CONCLUSIONS

This study presents PeLCV and DiYVB as a new natural combination resulting in leaf curl disease on P. atkinsiana plants. Phylogenetic analysis, in addition to recent agricultural reports, identify PeLCV as an emerging broad host range Begomovirus that is resident in Pakistan and, more recently, has also spread to India. Recombination analysis showed that PeLCV was involved in a natural recombinational event leading to the evolution of two recombinant begomoviruses, RaLCuV and PaLCuV.

Engineering Molecular Immunity Against Plant Viruses

Genomic engineering has been used to precisely alter eukaryotic genomes at the single-base level for targeted gene editing, replacement, fusion, and mutagenesis, and plant viruses such as Tobacco rattle virus have been developed into efficient vectors for delivering genome-engineering reagents. In addition to altering the host genome, these methods can target pathogens to engineer molecular immunity. Indeed, recent studies have shown that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems that target the genomes of DNA viruses can interfere with viral activity and limit viral symptoms in planta, demonstrating the utility of this system for engineering molecular immunity in plants. CRISPR/Cas9 can efficiently target single and multiple viral infections and confer plant immunity. Here, we discuss the use of site-specific nucleases to engineer molecular immunity against DNA and RNA viruses in plants. We also explore how to address the potential challenges encountered when producing plants with engineered resistance to single and mixed viral infections.

Emerging threats of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies

Begomoviruses (family Geminiviridae) are responsible for extreme yield reduction in a number of economically important crops including medicinal and aromatic plants (MAPs). Emergence of new variants of viruses due to recombination and mutations in the genomes, modern cropping systems, introduction of susceptible plant varieties, global trade in agricultural products, and changes in climatic conditions are responsible for aggravating the begomovirus problems during the last two decades. This review summaries the current research work on begomoviruses affecting MAPs and provides various traditional and advanced strategies for the management of begomoviruses and vector in MAPs.

Molecular characterization of Chilli leaf curl viruses infecting new host plant Petunia hybrida in India

Petunia hybrida is an important ornamental plant grown in many countries including India. It is a good model plant for the study of genetics and molecular biology. During a survey in 2013-2014, severe leaf curling was observed on most of the P. hybrida grown in the Sikar district, Rajasthan. The infected plants were analyzed for begomovirus infection by rolling circular amplification (RCA) and sequenced. Full length sequences confirmed the association of monopartite begomovirus with betasatellites. Phylogenetic analysis showed the highest percentage of identity with Chilli leaf curl virus (ChLCuV) and therefore considered to be an isolate of ChLCuV. Recombination analysis showed that ChLCuV has broadened its host range by recombination process. To the best our knowledge, this is the first report of natural occurrence of ChLCuV on P. hybrida in India.