scholarly journals High Throughput Sequencing-Aided Survey Reveals Widespread Mixed Infections of Whitefly-Transmitted Viruses in Cucurbits in Georgia, USA

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 988
Author(s):  
Saritha Raman Kavalappara ◽  
Hayley Milner ◽  
Naga Charan Konakalla ◽  
Kaelyn Morgan ◽  
Alton N. Sparks ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Mixed Infections ◽  
Genome Sequences ◽  
Rna Sequences ◽  
Southeastern Usa ◽  
Coding Regions ◽  
The Usa ◽  
Cucurbit Leaf Crumple Virus ◽  
Cucurbit Chlorotic Yellows Virus

Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.

Small RNA and transcriptome sequencing of a symptomatic peony plant reveals mixed infections with novel viruses

Plant Disease ◽  
2021 ◽  
Author(s):  
Anning Jia ◽  
Chenge Yan ◽  
Hang Yin ◽  
Rui Sun ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Triple Gene Block ◽  
Field Investigation ◽  
Mixed Infections ◽  
Species Classification ◽  
Gene Block ◽  
Sequence Identity

To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus (CNSV), apple stem grooving virus (ASGV), lychnis mottle virus (LycMoV), grapevine line pattern virus (GLPV), and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleaotides (nt) in length, comprising three open reading frames (ORFs) and shared 63.8–75.9% nucleotide sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57% and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length with five ORFs encoding the REP (ORF1), triple gene block (TGB, ORF2–4) and coat protein (CP, ORF5) proteins. Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus (GYMaV) within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.

scholarly journals The population structure of Rose rosette virus in the USA

2020 ◽  
Vol 101 (6) ◽  
pp. 676-684 ◽  
Author(s):  
Asimina Katsiani ◽  
Daisy Stainton ◽  
Kurt Lamour ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Population Structure ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Sequence Information ◽  
Coding Regions ◽  
Protein Length ◽  
Recent Emergence ◽  
Indel Polymorphisms ◽  
The Usa ◽  
Rose Rosette

Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5′ and 3′ non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.

scholarly journals Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Derek Toms ◽  
Bo Pan ◽  
Yinshan Bai ◽  
Julang Li
Keyword(s):  
Granulosa Cells ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Ovarian Function ◽  
Ovarian Follicle ◽  
Small Rna Sequencing ◽  
Cell Fractionation ◽  
Steroid Synthesis ◽  
Non Coding Rna ◽  
Dna Binding Sites

AbstractNuclear small RNAs have emerged as an important subset of non-coding RNA species that are capable of regulating gene expression. A type of small RNA, microRNA (miRNA) have been shown to regulate development of the ovarian follicle via canonical targeting and translational repression. Little has been done to study these molecules at a subcellular level. Using cell fractionation and high throughput sequencing, we surveyed cytoplasmic and nuclear small RNA found in the granulosa cells of the pig ovarian antral preovulatory follicle. Bioinformatics analysis revealed a diverse network of small RNA that differ in their subcellular distribution and implied function. We identified predicted genomic DNA binding sites for nucleus-enriched miRNAs that may potentially be involved in transcriptional regulation. The small nucleolar RNA (snoRNA) SNORA73, known to be involved in steroid synthesis, was also found to be highly enriched in the cytoplasm, suggesting a role for snoRNA species in ovarian function. Taken together, these data provide an important resource to study the small RNAome in ovarian follicles and how they may impact fertility.

scholarly journals Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1304
Author(s):  
Nicolás Bejerman ◽  
Ralf G. Dietzgen ◽  
Humberto Debat
Keyword(s):  
Plant Species ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
The Novel ◽  
Coding Regions ◽  
Public Data ◽  
Invaluable Tool ◽  
Sequencing Platforms ◽  
Viral Sequences ◽  
Plant Rhabdovirus

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

A global phylogenetic analysis of Japanese tonsil-derived Epstein–Barr virus strains using viral whole-genome cloning and long-read sequencing

2021 ◽  
Author(s):  
Misako Yajima ◽  
Risako Kakuta ◽  
Yutaro Saito ◽  
Shiori Kitaya ◽  
Atsushi Toyoda ◽  
...  
Keyword(s):  
Viral Genome ◽  
Epstein Barr Virus ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Regional Distribution ◽  
Genome Sequences ◽  
Barr Virus ◽  
Endemic Areas ◽  
Epstein Barr ◽  
Genome Heterogeneity

Epstein–Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.

scholarly journals Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs

2020 ◽  
Vol 11 ◽  
Author(s):  
Huimin Liu ◽  
Zhibin Shi ◽  
Chunguo Liu ◽  
Pengfei Wang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Pseudorabies Virus ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Full Genome Sequence ◽  
Genome Sequences ◽  
Protein Coding ◽  
One Step ◽  
Human Infections ◽  
Full Length Genome

Pseudorabies viruses (PRVs) pose a great threat to the pig industry of many countries around the world. Human infections with PRV have also been reported occasionally in China. Therefore, understanding the epidemiology and evolution of PRVs is of great importance for disease control in the pig populations and humans as well. In this study, we isolated a PRV designated HLJ-2013 from PRV-positive samples that had been collected in Heilongjiang, China, in 2013. The full genome sequence of the virus was determined to be ∼143 kbp in length using high-throughput sequencing. The genomic sequence identities between this isolate and 21 other previous PRV isolates ranged from 92.4% (with Bartha) to 97.3% (with SC). Phylogenetic analysis based on the full-length genome sequences revealed that PRV HLJ-2013 clustered together with all the Chinese strains in one group belonging to Genotype II, but this virus occurred phylogenetically earlier than all the other Chinese PRV strains. Phylogenetic trees based on both protein-coding genes and non-coding regions revealed that HLJ-2013 probably obtained its genome sequences from three origins: a yet unknown parent virus, the European viruses, and the same ancestor of all Chinese PRVs. Recombination analysis showed that HLJ-2013-like virus possibly donated the main framework of the genome of the Chinese PRVs. HLJ-2013 exhibited cytopathic and growth characteristics similar to that of the Chinese PRV strains SC and HeN1, but its pathogenicity in mice was higher than that of SC and lower than that of HeN1. The identification of HLJ-2013 takes us one step closer to understanding the origin of PRVs in China and provides new knowledge about the evolution of PRVs worldwide.

Raffaelea lauricola (laurel wilt).

2021 ◽  
Author(s):  
Stephen Fraedrich
Keyword(s):  
Solid Wood ◽  
Persea Americana ◽  
South Florida ◽  
Florida Current ◽  
Natural Ecosystems ◽  
Laurel Wilt ◽  
Southeastern Usa ◽  
Raffaelea Lauricola ◽  
Redbay Ambrosia Beetle ◽  
The Usa

Abstract Laurel wilt is responsible for the death of hundreds of millions of redbay (Persea borbonia sensu lato) trees throughout the southeastern USA, and the disease is also having significant effects on other species such as sassafras (Sassafras albidum) in natural ecosystems and avocado (Persea americana) in commercial production areas of south Florida. Laurel wilt is caused by the pathogen Raffaelea lauricola, a fungal symbiont of the redbay ambrosia beetle, Xyleborus glabratus. Thus far, the disease is confined to members of the Lauraceae that are native to the USA, or native to such places as the Caribbean, Central America and Europe and grown in the USA. The beetle and fungus are native to Asia and were likely introduced with untreated solid wood packing material at Port Wentworth, Georgia in the early 2000s. Since that time laurel wilt has spread rapidly in the coastal plains of the southeastern USA, spreading north into central North Carolina, as far west as Texas, and reaching the southernmost counties of Florida. Current models suggest that X. glabratus can tolerate temperature conditions that occur throughout much of the eastern USA, and so the disease threatens sassafras throughout much of this region. The disease poses a threat to lauraceous species indigenous to other areas of the Americas as well as Europe and Africa.

scholarly journals piRNA and Transposon Dynamics in Drosophila: A Female Story

2020 ◽  
Vol 12 (6) ◽  
pp. 931-947 ◽  
Author(s):  
Bastien Saint-Leandre ◽  
Pierre Capy ◽  
Aurelie Hua-Van ◽  
Jonathan Filée
Keyword(s):  
Small Rna ◽  
Drosophila Simulans ◽  
Genomic Context ◽  
Genome Sequences ◽  
Genomic Features ◽  
Male Germline ◽  
Recent Activity ◽  
Pirna Pathway ◽  
Female Germline ◽  
The Relationship

Abstract The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.

scholarly journals Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 954
Author(s):  
György Pasztor ◽  
Zsuzsanna Galbacs N. ◽  
Tamas Kossuth ◽  
Emese Demian ◽  
Erzsebet Nadasy ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Seed Dormancy ◽  
High Throughput ◽  
Small Rna ◽  
Diagnostic Method ◽  
High Throughput Sequencing ◽  
Infection Risk ◽  
Viral Diseases ◽  
Crop Fields ◽  
Special Control

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

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