Diverse begomovirus-betasatellite complexes cause tomato leaf curl disease in the western India

Discovery of a novel alphasatellite of the genus Clecrusatellite associated with a wide array of New World tomato-infecting begomoviruses

A new alphasatellite was discovered via high-throughput sequencing in mixed infections with five distinct tomato-infecting begomoviruses in central Brazil, and the presence of this alphasatellite in tomato leaf samples was confirmed by PCR and Sanger sequencing. It has a circular genome of 1,321 nucleotides with typical features of alphasatellites belonging to the subfamily Geminialphasatellitinae, including a replication-associated hairpin sequence (TAGTATTAC) and an open reading frame encoding a replication-associated protein. Pairwise sequence comparisons and phylogenetic analysis indicated that this alphasatellite represents a new species, with 69-77% sequence identity to other members of the genus Clecrusatellite. Tomato golden vein virus (TGVV) was the only begomovirus present in all six positive samples. However, it was not possible to determine which of these viruses can function as a helper virus for the alphasatellite. The species name "Clecrusatellite solanumbrasiliensis" is proposed to classify this alphasatellite associated with endemic Brazilian begomoviruses. To our knowledge, this is the first report of a tomato-associated alphasatellite in the New World.

Recombination, phylogenetic insights and co-existence dynamics of begomoviruses and satellite DNAs: implications for tomato viral disease management

BACKGROUND

Tomato leaf curl viral disease (ToLCV) is a major biotic stress, threatening tomato cultivation. However, limited information exists on the prevalence and diversity of ToLCV in Tamil Nadu, India and hence this study focused on identifying and characterizing such begomoviruses.

METHODS AND RESULTS

Tomato samples with infected symptoms were collected from major tomato-growing tracts of Tamil Nadu during 2023 to 2024 and subjected to polymerase chain reaction (PCR) using degenerate primers specific to ToLCV. Further, by employing rolling circle amplification (RCA), full-length sequences of viral genomes (∼2.7 kb), alphasatellites and betasatellites (∼1.35 kb each) were also obtained for three samples collected from different locations of Tamil Nadu (Dharmapuri (DPI-03), Krishnagiri (KGI-01) and Salem (SLM-01)). Diverse begomoviruses, including tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Palampur virus (ToLCPalV), tomato leaf curl Bangalore virus (ToLCBaV), and tomato leaf curl Gujarat virus (ToLCGUV) were identified in these three samples. Additionally, an alphasatellite (cotton leaf curl Multan alphasatellite, CLCuMuA), and two betasatellites (tomato leaf curl Bangalore betasatellite, ToLCBaB and tomato leaf curl Gujarat betasatellite, ToLCGUB) were also identified in KGI-01 and SLM-01. Evaluation of phylogenetic relationship and genetic variability revealed distinct clustering of begomoviruses and satellite sequences with high nucleotide diversity. In addition, recombinant analysis predicted inter- and intra- species recombination events.

CONCLUSION

This study identified the co-occurrence of ToLCNDV with ToLCPalV, ToLCBaV with CLCuMuA and ToLCBaB, and ToLCGUV with ToLCGUB within the same plants. These findings underscore the diverse nature of the begomovirus-satellite complex infecting tomatoes in Tamil Nadu and emphasize the urgent need to develop effective plant protection strategies.

Demonstration of Insect Vector-Mediated Transfer of a Betasatellite between Two Helper Viruses

Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread and association of these molecules with helper viruses in host plants are thus matters of concern. Here, we focus on the propagation of betasatellites and, more specifically, on their transfer between different helper viruses and hosts through vector transmission. Our results show that the cotton leaf curl Gezira betasatellite (CLCuGeB), initially acquired with its helper virus cotton leaf curl Gezira virus (CLCuGeV) from an okra plant, can be transmitted and assisted by a different helper virus, tomato yellow leaf curl virus (TYLCV), in a different host plant (tomato plant). The new association can be formed whether TYLCV and CLCuGeB encounter each other in a host plant previously infected with TYLCV or in whiteflies having acquired the different components separately. Our findings reveal two pathways by which betasatellites can be transferred between helper viruses and host plants and highlight the ability of betasatellites to spread in begomovirus-infected environments.

Transreplication Preference of the Tomato Leaf Curl Joydebpur Virus for a Noncognate Betasatellite through Iteron Resemblance on Nicotiana bethamiana

Pepper plants (Capsicum annuum) with severe leaf curl symptoms were collected in 2013 from Bangalore, Karnataka, India. The detection results showed a co-infection between the tomato leaf curl Joydebpur virus (ToLCJoV) and tomato leaf curl Bangladesh betasatellite (ToLCBDB) through the sequencing analysis of PCR amplicons. To pinpoint the molecular mechanism of this uncommon combination, infectious clones of ToLCJoV and two different betasatellites-ToLCBDB and tomato leaf curl Joydebpur betasatellite (ToLCJoB)-were constructed and tested for their infectivity in Nicotiana benthamiana. Together, we conducted various combined agroinoculation studies to compare the interaction of ToLCJoV with non-cognate and cognate betasatellites. The natural non-cognate interaction between ToLCJoV and ToLCBDB showed severe symptoms compared to the mild symptoms of a cognate combination (ToLCJoV × ToLCJoB) in infected plants. A sequence comparison among betasatellites and their helper virus wasperformed and the iteron resemblances in ToLCBDB as well as ToLCJoB clones were processed. Mutant betasatellites that comprised iteron modifications revealed that changes in iteron sequences could disturb the transreplication process between betasatellites and their helper virus. Our study might provide an important consideration for determining the efficiency of transreplication activity between betasatellites and their helper virus.

A distinct strain of tomato leaf curl New Delhi virus that causes mosaic disease in ash gourd and other cucurbitaceous crops

Ash gourd (Benincasa hispida) is a cucurbitaceous crop cultivated as an edible vegetable rich in vitamins, minerals, dietary fibers and antioxidants. In a field survey conducted in the Udumalpet region of Tamil Nadu during 2019, the incidence of mosaic disease on ash gourd crop was observed to be 75%. The DNA-A and DNA-B components of begomovirus genome have been identified as associated with this disease. Both the cloned DNA-A and DNA-B genomic components shared highest pairwise sequence identities with the isolates of tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus. Recombinant analysis showed that both the components are possibly evolved through intra-species recombination between ToLCNDV isolates. Tomato leaf curl Bangladesh betasatellite (ToLCBB) is not naturally associated with this sample. The results of infectivity studies on ash gourd and other cucurbitaceous crops demonstrates the Koch's postulates, when co-inoculation of DNA-A and DNA-B of ToLCNDV was undertaken. However, the inoculation of non-cognate ToLCBB along with DNA-A and DNA-B enhances the symptom expression and reduces the time taken for symptom development. Thus, Koch's postulates were proved for these virus complexes on cucurbitaceous crops. Furthermore, an enhanced accumulation of DNA-A component was detected in the cucurbits co-inoculated with ToLCNDV and ToLCBB. This report highlights the importance of investigating the spread of these disease complexes with other cucurbitaceous crops in India.