Complete genome sequence of Jacquemontia yellow mosaic virus, a novel begomovirus from Venezuela related to other New World bipartite begomoviruses infecting Convolvulaceae

Insights into Emerging Begomovirus-Deltasatellite Complex Diversity: The First Deltasatellite Infecting Legumes

Begomoviruses and associated DNA satellites are involved in pathosystems that include many cultivated and wild dicot plants and the whitefly vector Bemisia tabaci. A survey of leguminous plants, both crops and wild species, was conducted in Venezuela, an understudied country, to determine the presence of begomoviruses. Molecular analysis identified the presence of bipartite begomoviruses in 37% of the collected plants. Four of the six begomoviruses identified constituted novel species, and two others had not been previously reported in Venezuela. In addition, a novel deltasatellite (cabbage leaf curl deltasatellite, CabLCD) was found to be associated with cabbage leaf curl virus (CabLCV) in several plant species. CabLCD was the first deltasatellite found to infect legumes and the first found in the New World to infect a crop plant. Agroinoculation experiments using Nicotiana benthamiana plants and infectious viral clones confirmed that CabLCV acts as a helper virus for CabLCD. The begomovirus-deltasatellite complex described here is also present in wild legume plants, suggesting the possible role of these plants in the emergence and establishment of begomoviral diseases in the main legume crops in the region. Pathological knowledge of these begomovirus-deltasatellite complexes is fundamental to develop control methods to protect leguminous crops from the diseases they cause.

Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories

In the Caribbean Basin, malvaceous weeds commonly show striking golden/yellow mosaic symptoms. Leaf samples from Malachra sp. and Abutilon sp. plants with these symptoms were collected in Hispaniola from 2014 to 2020. PCR tests with degenerate primers revealed that all samples were infected with a bipartite begomovirus, and sequence analyses showed that Malachra sp. plants were infected with tobacco leaf curl Cuba virus (TbLCuCV), whereas the Abutilon sp. plants were infected with a new bipartite begomovirus, tentatively named Abutilon golden yellow mosaic virus (AbGYMV). Phylogenetic analyses showed that TbLCuCV and AbGYMV are distinct but closely related species, which are most closely related to bipartite begomoviruses infecting weeds in the Caribbean Basin. Infectious cloned DNA-A and DNA-B components were used to fulfilled Koch's postulates for these diseases of Malachra sp. and Abutilon sp. In host range studies, TbLCuCV also induced severe symptoms in Nicotiana benthamiana, tobacco and common bean plants; whereas AbGYMV induced few or no symptoms in plants of these species. Pseudorecombinants generated with the infectious clones of these viruses were highly infectious and induced severe symptoms in N. benthamiana and Malachra sp., and both viruses coinfected Malachra sp., and possibly facilitating virus evolution via recombination and pseudorecombination. Together, our results suggest that TbLCuCV primarily infects Malachra sp. in the Caribbean Basin, and occasionally spills over to infect and cause disease in crops; whereas AbGYMV is well-adapted to an Abutilon sp. in the Dominican Republic and has not been reported infecting crops.

Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela

Begomoviruses are one of the major groups of plant viruses with an important economic impact on crop production in tropical and subtropical regions. The global spread of its polyphagous vector, the whitefly Bemisia tabaci, has contributed to the emergence and diversification of species within this genus. In this study, we found a putative novel begomovirus infecting tomato plants in Venezuela without a cognate DNA-B component. This begomovirus was genetically characterized and compared with related species. Furthermore, its infectivity was demonstrated by agroinoculation of infectious clones in tomato (Solanum lycopersicum) and Nicotiana benthamiana plants. The name Tomato twisted leaf virus (ToTLV) is proposed. ToTLV showed the typical genome organization of the DNA-A component of New World bipartite begomoviruses. However, the single DNA component of ToTLV was able to develop systemic infection in tomato and N. benthamiana plants, suggesting a monopartite nature of its genome. Interestingly, an additional open reading frame ORF was observed in ToTLV encompassing the intergenic region and the coat protein gene, which is not present in other closely related begomoviruses. A putative transcript from this region was amplified by strand-specific reverse transcription-PCR. Along with recent studies, our results showed that the diversity of monopartite begomoviruses from the New World is greater than previously thought.

Complete genome sequence of jacquemontia yellow vein virus, a novel begomovirus infecting Jacquemontia tamnifolia in Venezuela

Wild plants of the family Convolvulaceae are hosts for a few New World begomoviruses (genus Begomovirus, family Geminiviridae). In this work, we report the complete genome sequence of a new begomovirus infecting the wild convolvulaceous plant Jacquemontia tamnifolia in Venezuela. The cloned bipartite genome showed the organization of typical New World begomoviruses and was found to be phylogenetically related to those of begomoviruses from Venezuela and other Caribbean countries. Several recombination events have been shown to have occurred involving genome fragment exchange with related begomoviruses infecting crops such as tomato and cucurbits and wild plants, including Jacquemontia sp. We propose the name jacquemontia yellow vein virus (JacYVV) for this new begomovirus.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).