Complete sequence of a new bipartite begomovirus infecting Sida sp. in Northeastern Brazil

The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding

Cotton (Gossypium spp. L., Malvaceae) is the world's largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.

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.

Intra-host evolution of the ssDNA virus tomato severe rugose virus (ToSRV)

To evaluate and quantify the evolutionary dynamics of the bipartite begomovirus tomato severe rugose virus (ToSRV) in a cultivated and a non-cultivated host, plants of tomato and Nicandra physaloides were biolistically inoculated with an infectious clone and systemically infected leaves were sampled at 30, 75 and 120 days after inoculation. Total DNA was extracted and sequenced in the Illumina HiSeq 2000 platform. The datasets were trimmed with the quality score limit set to 0.01, and the assembly was performed using the infectious clone sequence as reference. SNPs were filtered using a minimum p-value of 0.001 and the sum frequencies were used to calculate the deviation from the original clone sequence. Nucleotide substitution rates were calculated for the two DNA components in both hosts: 1.73 × 10^-3 and 3.07 × 10^-4 sub/site/year for the DNA-A and DNA-B, respectively, in N. physaloides, and 8.05 × 10^-4 and 7.02 × 10^-5 sub/site/year the for DNA-A and DNA-B, respectively, in tomato. These values are in the same range of those estimated for viruses with single-stranded RNA genomes and for other begomoviruses. Strikingly, the number of substitutions decreased over time, suggesting the presence of bottlenecks during systemic infection. Determination of Shannon's entropy indicated different patterns of variation in the DNA-A and the DNA-B, suggesting distinct evolutionary forces acting upon each component.