From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species.

Viruses comprise the most abundant genetic material in the biosphere; however, global viral genomic population (virome) has been largely underestimated. Recently, high-throughput sequencing (HTS) has provided a powerful tool for the detection of known viruses and the discovery of novel viral species from environmental and individual samples using metagenomics and ecogenomics approaches, respectively. Viruses with circular DNA single-stranded (ssDNA) genomes belonging to the begomovirus genera (family Geminiviridae) constitute the largest group of emerging plant viruses worldwide.

Quantification of Virion-Sense and Complementary-Sense DNA Strands of Circular Single-Stranded DNA Viruses.

Circular ssDNA viruses are ubiquitous and can be found in both prokaryotes and eukaryotes. To understand the interaction of ssDNA viruses with their hosts, it is important to characterize the dynamics of viral sense (VS) and complementary-sense (CS) viral strands during the infection process. Here, we present a simple and rapid protocol that allows sensitive and accurate determination of the VS and CS strands generated during viral infection.

First report of Pectobacterium polaris causing aerial stem rot of potato in Mexico.

In Mexico, potato (Solanum tuberosum L.) is one of the most important vegetable crops for local consumption and industry. More than 1.

A novel tomato spotted wilt virus isolate encoding a noncanonical NSm C118F substitution associated with Sw-5 tomato gene resistance breaking.

The nonstructural protein NSm of tomato spotted wilt virus (TSWV) has been identified as the avirulence determinant of the tomato single dominant Sw-5 resistance gene. Although Sw-5 effectiveness has been shown for most TSWV isolates, the emergence of resistance-breaking (RB) isolates has been observed. It is strongly associated with two point mutations (C118Y or T120N) in the NSm viral protein.

Differential Expression of miRNAs Involved in Response to Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease.

Huanglongbing (HLB) is one of the most destructive diseases threatening citriculture worldwide. This disease has been associated with α-proteobacteria species, namely Liberibacter. Due to the unculturable nature of the causal agent, it has been difficult to mitigate the disease, and nowadays a cure is not available.

From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico.

Begomoviruses (Family ) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases.

miR825-5p targets the TIR-NBS-LRR gene MIST1 and down-regulates basal immunity against Pseudomonas syringae in Arabidopsis.

Plants encode numerous intracellular receptors known as nucleotide-binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived effectors or their activity to activate defenses. miRNAs regulate NLR genes in many species, often triggering the production of phased siRNAs (phasiRNAs). Most such examples involve genes encoding NLRs carrying coiled-coil domains, although a few include genes encoding NLRs carrying a Toll/interleukin-1 domain (TNL).

Cucurbit leaf crumple virus (CuLCrV) associated to watermelon disease in Campeche state, Mexico.

An annual recurrent disease causing yield reduction in cultivated watermelon (Citrullus lanatus) was documented by the growers in different farms of Campeche state, Mexico. In April 2019 and March 2020 open field grown watermelon plants showed symptoms such as leaf curling, crumpling, and leaf basal or apical necrosis (Figure S1), with an incidence ranging from 30 up to 80%. These plants also presented high populations of whitefly, especially in the most affected fields.

Characterization of Curtovirus V2 Protein, a Functional Homolog of Begomovirus V2.

Geminiviruses are single-stranded DNA plant viruses with circular genomes packaged within geminate particles. Among the family, and comprise the two best characterized genera. Curtovirus and Old World begomovirus possess similar genome structures with six to seven open-reading frames (ORF).

Gene Expression Profile of Mexican Lime () Trees in Response to Huanglongbing Disease caused by Liberibacter asiaticus.

Nowadays, Huanglongbing (HLB) disease, associated with Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host-pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited.

Superinfection by PHYVV Alters the Recovery Process in PepGMV-Infected Pepper Plants.

Geminiviruses are important plant pathogens that affect crops around the world. In some geminivirus-host interactions, infected plants show recovery, a phenomenon characterized by symptom disappearance in newly emerging leaves. In pepper- (PepGMV) interaction, the host recovery process involves a silencing mechanism that includes both post-transcriptional (PTGS) and transcriptional (TGS) gene silencing pathways.

assembly and functional annotation of transcriptome from Liberibacter asiaticus infected and non-infected trees.

Mexican lime () belongs to the Rutaceae family and nowadays is one of the major commercial citrus crops in different countries. In Mexico, Mexican lime production is impaired by Huanglongbing (HLB) disease associated to Liberibacter asiaticus (CLas) bacteria. To date, transcriptomic studies of CLas-Citrus interaction, have been performed mainly in sweet citrus models at symptomatic (early) stage where pleiotropic responses could mask important, pathogen-driven host modulation as well as, host antibacterial responses.

The Peptide AmPep1 Derived from Amaranth Recognizes the Replication Hairpin of TYLCV Disturbing Its Replication Process in Host Plants.

Antiviral compounds targeting viral replicative processes have been studied as an alternative for the control of begomoviruses. Previously, we have reported that the peptide AmPep1 has strong affinity binding to the replication origin sequence of tomato yellow leaf curl virus (TYLCV). In this study, we describe the mechanism of action of this peptide as a novel alternative for control of plant-infecting DNA viruses.

High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico.

Plant DNA viruses of the genus have been documented as the most genetically diverse in the family and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012-2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming.

V2 from a curtovirus is a suppressor of post-transcriptional gene silencing.

The suppression of gene silencing is a key mechanism for the success of viral infection in plants. DNA viruses from the Geminiviridae family encode several proteins that suppress transcriptional and post-transcriptional gene silencing (TGS/PTGS). In Begomovirus, the most abundant genus of this family, three out of six genome-encoded proteins, namely C2, C4 and V2, have been shown to suppress PTGS, with V2 being the strongest PTGS suppressor in transient assays.

Tomato yellow leaf curl virus: No evidence for replication in the insect vector Bemisia tabaci.

Begomovirus ssDNA plant virus (family Geminiviridae) replication within the Bemisia tabaci vector is controversial. Transovarial transmission, alteration to whitefly biology, or detection of viral transcripts in the vector are proposed as indirect evidence of replication of tomato yellow leaf curl virus (TYLCV). Recently, contrasting direct evidence has been reported regarding the capacity of TYLCV to replicate within individuals of B.

Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery).

Unlabelled: Geminiviruses are important plant pathogens characterized by circular, single-stranded DNA (ssDNA) genomes. However, in the nuclei of infected cells, viral double-stranded DNA (dsDNA) associates with host histones to form a minichromosome. In phloem-limited geminiviruses, the characterization of viral minichromosomes is hindered by the low concentration of recovered complexes due to the small number of infected cells.

A sensitive method for the quantification of virion-sense and complementary-sense DNA strands of circular single-stranded DNA viruses.

Circular single-stranded DNA (ssDNA) viruses are the smallest viruses known to infect eukaryotes. High recombination and mutation rates have conferred these viruses with an evolutionary potential that has facilitated their emergence. Their damaging effects on livestock (circoviruses) and crops (geminiviruses and nanoviruses), and the ubiquity of anelloviruses in human populations and other mammalian species, have resulted in increased interest in better understanding their epidemiology and infection mechanisms.

C2 from Beet curly top virus promotes a cell environment suitable for efficient replication of geminiviruses, providing a novel mechanism of viral synergism.

• Geminiviruses are plant viruses with circular, single-stranded (ss) DNA genomes that infect a wide range of species and cause important losses in agriculture. Geminiviruses do not encode their own DNA polymerase, and rely on the host cell machinery for their replication. • Here, we identify a positive effect of the curtovirus Beet curly top virus (BCTV) on the begomovirus Tomato yellow leaf curl Sardinia virus (TYLCSV) infection in Nicotiana benthamiana plants.

RNA silencing against geminivirus: complementary action of posttranscriptional gene silencing and transcriptional gene silencing in host recovery.

RNA silencing in plants is a natural defense system mechanism against invading nucleic acids such as viruses. Geminiviruses, a family of plant viruses characterized by a circular, single-stranded DNA genome, are thought to be both inducers and targets of RNA silencing. Some natural geminivirus-host interactions lead to symptom remission or host recovery, a process commonly associated with RNA silencing-mediated defense.