Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences

Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.

Advances in understanding the biology and epidemiology of barley yellow dwarf virus (BYDV)

A tri-trophic network of domesticated grasses (host), various aphids (vector) and barley yellow dwarf virus (pathogen) species has been spread by humans from Eurasia to the rest of the world. Understanding how climate, natural and agricultural landscapes challenge pathogens, vectors, and their natural enemies and shape their dynamics is the key to managing this pathosystem. This chapter provides an overview of this complex system and its evolution. The chapter includes a case study of biological control of aphids causing wheat BYDV in Brazil. The current challenge is to create tools that integrate knowledge of this complex pathosystem and facilitate monitoring and decision making for rational management to reduce the burden of disease.

Resistance breeding in barley against Barley yellow dwarf virus (BYDV): avoiding negative impacts on anatomy and physiology

Barley yellow dwarf (BYD) is one of the most widespread and damaging viral diseases of grasses and cereal crops worldwide. Due to an increasing risk of food losses e.g. in barley by Barley yellow dwarf virus (BYDV) as a consequence of climate change, associated by a strong demand to decrease the use of chemical insecticides, breeding for BYDV resistance is of prime importance today. This chapter describes the negative impact of BYDV on barley on multiple levels (anatomy, physiology and agronomic traits). It also demonstrates the benefits of BYDV resistance regarding a reduction in yield losses but also a decreased spread of BYDV in the field due to effects on the tritrophic interaction of virus, vector and plant. Until now, several genes and QTL are known that mediate tolerance or resistance against BYDV, respectively. The combination of genomic tools and phenotyping is the basis for the identification of these genes and recent developments facilitate to enhance this process.

Nucleus

In our application of AuNPs on the leaf surface, we were pushing the Barley Yellow Dwarf Virus (BYDV-PAV) source and Gold nanoparticles (AuNPs) into the plant cell system up on the events of systemic plant defense response. In the infected host cell, the viral coat protein is the first obvious in the cytoplasm. When nanoparticles are applied on leaf surfaces, a large surface area relative to their volume happens. AuNPs solutions are more active and dispersed ooplasm. The correlation between Zeta potential value and Zeta sizer is inverse proportion. Filaments are visible in the nucleopores, the nuclear outline is distorted, and massive clumping of heterochromatin begins as declared. It was mostly found in or around regions of ribosome-associated filaments. Our present study combines TEM and nucleus content in the presence of AuNPS to explore the level of repair mechanism illustrating in TEM micrographs, showing Polyploidy nucleus and segregated chromatin. Multi membranous structure, imaging the AuNPs inside and around the nucleus and Pseudo crystal array is enveloped in an endoplasmic reticulum cisterna (ER).

Cell Wall

The application of AuNPs on the infected barley cultivar had great damage results on Barley Yellow Dwarf Virus (BYDV-PAV) particles in TEM. Observation of TEM images provided an insight into the transport of AuNPs through the plasmodesmata endoplasmic reticulum route, where they likely accumulated as the channels narrowed. The cytoplasmic parenchyma cell components do not have an intact peripheral location, but taking irregular shapes, internal movement between adjacent two cells seems to be the VLPs moved toward via plasmodesmata. TEM micrographs; showing different abnormalities in the cell wall due to viral infection. Application of AuNPs revealed sticky Integrated AuNPs inside the cell wall with low and high density. The mechanical transportation of the virus through the sieve elements with endosomes was observed. The mechanical transportation of virus particles through the cell wall with some vesicles, amorphous inclusions, and filamentous particles was proved through the sieve elements with filamentous strands.

Chloroplast and Mitochondria

Photosynthesis is a crucial process for plants on earth that changes light energy to chemical energy. Virus infection can cause dramatic photosynthesis changes: respiration and the translocation of carbohydrates and other substances around the host plant. Chlorosis in virus-infected leaves like Barley Yellow Dwarf Virus (BYDV- PAV).infection can result from damage to chloroplasts resulting from inhibition of photosynthetic activity. Our present study combines TEM and chlorophyll-level content in the presence of Gold nanoparticles (AuNPS) to explore the repair mechanism for the yellowing leaf symptom development caused by infection with BYDV- PAV by illustrating TEM micrographs; showing fragmentized grana, deformation of the myelin like bodies (MLB), many vesicles; osmiophilic lipid granules/plastoglobulus, starch body, and plasmolysis in the chloroplast, distribution of AuNPs & VLPs near and inside the chloroplast. Mitochondria, Double-membrane-bound organelle, Distorted mitochondrion, Amorphous inclusion bodies.

Cytoplasmic Matrix and Viroplasms Inclusions in the Presence of Gold Nanoparticles (AuNPs)

Cellular ultrastructure micrographs revealed striking changes resulting from the Barley Yellow Dwarf Virus (BYDV-PAV) infection in Electron microscopy. In the cytoplasm, the Gold nanoparticles (AuNPs) may bind with different cytoplasmic organelles and interfere with the treated site’s metabolic processes. The micrographs of the treated plant leave with AuNPs showing; Endosomes, amorphous bodies, slender filaments fibers, myelin bodies with a high concentration of virus particles, and Gold Nanoparticles distributed in a circulated shape in the cytoplasm with virus particles.