scholarly journals New World Cactaceae Plants Harbor Diverse Geminiviruses

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 694
Author(s):  
Rafaela S. Fontenele ◽  
Andrew M. Salywon ◽  
Lucas C. Majure ◽  
Ilaria N. Cobb ◽  
Amulya Bhaskara ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Scale Insects ◽  
Mixed Infections ◽  
Virus Species ◽  
Protein Database ◽  
Clear Trend ◽  
Refseq Protein ◽  
Cultivated Species ◽  
Ecological Importance ◽  
Succulent Plants

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

scholarly journals Graft-transmissible diseases of Ribes – pathogens, impact and control

Plant Disease ◽  
2020 ◽  
Author(s):  
Josef Spak ◽  
Igor Koloniuk ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
New Species ◽  
High Throughput Sequencing ◽  
Control Measures ◽  
Mixed Infections ◽  
Virus Species ◽  
New Era ◽  
Ribes Spp ◽  
And Control ◽  
Propagation Material

This article provides an up-to-date review of disease causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Ca. Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.

scholarly journals First report of Cherry virus F infecting Japanese plum in Korea

Plant Disease ◽  
2020 ◽  
Author(s):  
Yeonhwa Jo ◽  
Hoseong Choi ◽  
Jin Kyong Cho ◽  
Won Kyong Cho
Keyword(s):  
Czech Republic ◽  
High Throughput Sequencing ◽  
Prunus Avium ◽  
De Novo ◽  
Protein Database ◽  
Specific Primers ◽  
The Czech Republic ◽  
First Report ◽  
Japanese Plum ◽  
Leaf Spots

Cherry virus F (CVF) is a tentative member of the genus Fabavirus in the family Secoviridae, consisting of two RNA segments (Koloniuk et al. 2018). To date, CVF has been documented in only sweet cherry (Prunus avium) in the Czech Republic (Koloniuk et al. 2018), Canada, and Greece. In May 2014, we collected leaf samples from four symptomatic (leaf spots and dapple fruits) and two asymptomatic Japanese plum cultivars (Sun and Gadam) grown in an orchard in Hoengseong, South Korea, to identify viruses and viroids infecting plum trees. Total RNA from individual plum trees was extracted using two commercial kits: Fruit-mate for RNA Purification Kit (Takara, Shiga, Japan) and RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). We generated six mRNA libraries from the six different plum cultivars for RNA-sequencing using the TruSeq RNA Library Preparation Kit v2 (Illumina, CA, U.S.A.) as described previously (Jo et al. 2017). The mRNA libraries were paired-end (2 X 100 bp) sequenced with a HiSeq 2000 system (Macrogen, Seoul, Korea). The raw sequence reads were de novo assembled by Trinity program v. 2.8.6, with default parameters (Haas et al. 2013). The assembled contigs were subjected to BLASTX search against the non-redundant protein database in NCBI. Of the two asymptomatic cultivars, the transcriptome of asymptomatic plum cv. Gadam contained five contigs specific to CVF. Two and three contigs were specific to CVF RNA1 (2,571 reads, coverage 42.15%) and RNA2 (2,025 reads, coverage 53.04%), respectively. The size of these five contigs ranged from 241 to 5,986 bp. Contigs of 5,986 and 3,867 bp in length, referred to as CVF isolate Gadam RNA1 (GenBank MN896996) and RNA2 (GenBank MN896995), respectively, were subjected to BLASTP search against NCBI’s non-redundant protein database. The results showed that the polyprotein sequences of RNA1 and RNA2 shared 95.3% and 93.11% amino acid identities with isolates SwC-H_1a from the Czech Republic (GenBank acc. no. AWB36326) and Stac-3B_c8 from Canada (AZZ10055), respectively. To confirm the infection of CVF in cv. Gadam, RT-PCR was conducted using CVF RNA1-specific primers designed based on the CVF reference genome sequences (MH998210 and MH998216), including 5’-CCACCAAATAGGCAAGAGGTCAC-3’ (position 3190–3212) and 5’-CACAATCACCATCAATGGTCTCTGC-3’ (position 3742–3766), and CVF RNA2-specific primers, including 5’-CTGCTTTATGATGCTAGACATCAAGATG-3’ (position 1015–1042) and 5’-ACAATAGGCATGCTCATCTCAACCTC-3’ (position 1594–1619). We amplified 577-bp RNA1-specific and 605-bp RNA2-specific amplicons that were cloned and then performed Sanger sequencing. Sequencing of the cloned amplicons for isolate Gadam RNA1 (GenBank MN896993) and RNA2 (GenBank MN896994) revealed values of 99.48% and 99.17% nucleotide identity to that of RNA1 and RNA2 determined by high-throughput sequencing, respectively. Additionally, we tested five plants for each of the six plum cultivars grown in the same orchard. The detection of CVF was carried out through PCR using the primers and protocol described above. Of the 30 trees, CVF was detected in three trees of cv. Gadam by both primer pairs. To our knowledge, this is the first report of CVF infecting Japanese plum and the first report of the virus in Korea. However, its prevalence in other Prunus species, including apricot, European plum, and peach, should be further elucidated.

scholarly journals Identification of residue inversions in large phylogenies of duplicated proteins

2021 ◽  
Author(s):  
Stefano Pascarelli ◽  
Paola Laurino
Keyword(s):  
Gene Duplication ◽  
Protein Sequence ◽  
Protein Function ◽  
High Throughput Sequencing ◽  
Functional Divergence ◽  
Growth Factor Receptor ◽  
Sequence Evolution ◽  
Protein Database ◽  
Sequencing Studies ◽  
Homology Relationship

Connecting protein sequence to function is becoming increasingly relevant since high-throughput sequencing studies accumulate large amounts of genomic data. Protein database annotation helps to bridge this gap; however, it is fundamental to understand the mechanisms underlying functional inheritance and divergence. If the homology relationship between proteins is known, can we determine whether the function diverged? In this work, we analyze different possibilities of protein sequence evolution after gene duplication and identify "residue inversions", i.e., sites where the relationship between the ancestry and the functional signal is decoupled. Residues in these sites play a role in functional divergence and could indicate a shift in protein function. We develop a method to recognize residue inversions in a phylogeny and test it on real and simulated datasets. In a dataset built from the Epidermal Growth Factor Receptor (EGFR) sequences found in 88 fish species, we identify 19 positions that went through inversion after gene duplication, mostly located at the ligand-binding extracellular domain.

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 Thrips as the Transmission Bottleneck for Mixed Infection of Two Orthotospoviruses

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 509
Author(s):  
Kaixi Zhao ◽  
Cristina Rosa
Keyword(s):  
Genetic Diversity ◽  
Virus Replication ◽  
Mixed Infection ◽  
Viral Fitness ◽  
Mixed Infections ◽  
Virus Species ◽  
Necrotic Spot ◽  
Tomato Spotted Wilt ◽  
Transmission Bottleneck

Mixed infections provide opportunities for viruses to increase genetic diversity by facilitating genomic reassortment or recombination, and they may lead to the emergence of new virus species. Mixed infections of two economically important orthotospoviruses, Tomato spotted wilt orthotospovirus (TSWV) and Impatiens necrotic spot orthotospovirus (INSV), were found in recent years, but no natural reassortants between INSV and TSWV were ever reported. The goal of this study was to establish how vector preferences and the ability to transmit INSV and TSWV influence transmission and establishment of mixed infections. Our results demonstrate that thrips prefer to oviposit on TSWV and INSV mixed-infected plants over singly infected or healthy plants, providing young nymphs with the opportunity to acquire both viruses. Conversely, we observed that thrips served as a bottleneck during transmission and favored transmission of one of the two viruses over the second one, or over transmission of both viruses simultaneously. This constraint was relaxed in plants, when transmission of TSWV and INSV occurred sequentially, demonstrating that plants serve as orthotospovirus permissive hosts, while thrips serve as a bottleneck. Viral fitness, as measured by virus replication, transmission, and competition with other viral strains, is not well studied in mixed infection. Our study looks at the success of transmission during mixed infection of orthotopoviruses, enhancing the understanding of orthotospovirus epidemiology and evolution.

scholarly journals High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 820
Author(s):  
Julia Minicka ◽  
Aleksandra Zarzyńska-Nowak ◽  
Daria Budzyńska ◽  
Natasza Borodynko-Filas ◽  
Beata Hasiów-Jaroszewska
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Yellow Mosaic Virus ◽  
Virus Species ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
Detection And Identification ◽  
New Finding ◽  
Recent Occurrence

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

Were bivalves ecologically dominant over brachiopods in the late Paleozoic? A test using exceptionally preserved fossil assemblages

Paleobiology ◽  
2019 ◽  
Vol 45 (02) ◽  
pp. 265-279 ◽  
Author(s):  
Shannon Hsieh ◽  
Andrew M. Bush ◽  
J Bret Bennington
Keyword(s):  
Fossil Record ◽  
Energy Use ◽  
Regional Scale ◽  
Late Paleozoic ◽  
Ecosystem Structure ◽  
Relative Importance ◽  
Clear Trend ◽  
Fossil Assemblages ◽  
Ecological Importance ◽  
Preferential Dissolution

AbstractInterpreting changes in ecosystem structure from the fossil record can be challenging. In a prominent example, the traditional view that brachiopods were ecologically dominant over bivalves in the Paleozoic has been disputed on both taphonomic and metabolic grounds. Aragonitic bivalves may be underrepresented in many fossil assemblages due to preferential dissolution. Abundance counts may further understate the ecological importance of bivalves, which tend to have more biomass and higher metabolic rates than brachiopods. We evaluate the relative importance of the two clades in exceptionally preserved, bulk-sampled fossil assemblages from the Pennsylvanian Breathitt Formation of Kentucky, where aragonitic bivalves are preserved as shells, not molds. At the regional scale, brachiopods were twice as abundant as bivalves and were collectively equivalent in biomass and energy use. Analyses of samples from the Paleobiology Database that contain abundance counts are consistent with these results and show no clear trend in the relative ecological importance of bivalves during the middle and late Paleozoic. Bivalves were probably more important in Paleozoic ecosystems than is apparent in many fossil assemblages, but they were not clearly dominant over brachiopods until after the Permian–Triassic extinction, which caused the shelly benthos to shift from bivalve and brachiopod dominated to merely bivalve dominated.

scholarly journals Genomic Analyses of Cherry Rusty Mottle Group and Cherry Twisted Leaf-Associated Viruses Reveal a Possible New Genus Within the FamilyBetaflexiviridae

2015 ◽  
Vol 105 (3) ◽  
pp. 399-408 ◽  
Author(s):  
D. E. V. Villamor ◽  
J. Susaimuthu ◽  
K. C. Eastwell
Keyword(s):  
New Genus ◽  
High Throughput Sequencing ◽  
Prunus Avium ◽  
Triple Gene Block ◽  
Mottle Virus ◽  
Virus Species ◽  
Gene Block ◽  
Green Ring ◽  
The Family ◽  
Prunus Spp

It is demonstrated that closely related viruses within the family Betaflexiviridae are associated with a number of diseases that affect sweet cherry (Prunus avium) and other Prunus spp. Cherry rusty mottle-associated virus (CRMaV) is correlated with the appearance of cherry rusty mottle disease (CRMD), and Cherry twisted leaf-associated virus (CTLaV) is linked to cherry twisted leaf disease (CTLD) and apricot ringpox disease (ARPD). Comprehensive analysis of previously reported full genomic sequences plus those determined in this study representing isolates of CTLaV, CRMaV, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus revealed segregation of sequences into four clades corresponding to distinct virus species. High-throughput sequencing of RNA from representative source trees for CRMD, CTLD, and ARPD did not reveal additional unique virus sequences that might be associated with these diseases, thereby further substantiating the association of CRMaV and CTLaV with CRMD and CTLD or ARPD, respectively. Based on comparison of the nucleotide and amino acid sequence identity values, phylogenetic relationships with other triple-gene block-coding viruses within the family Betaflexiviridae, genome organization, and natural host range, a new genus (Robigovirus) is suggested.

scholarly journals Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1867
Author(s):  
Ziyi Wang ◽  
Achal Neupane ◽  
Jiuhuan Feng ◽  
Connor Pedersen ◽  
Shin-Yi Lee Marzano
Keyword(s):  
South Dakota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Resource ◽  
De Novo ◽  
Fungal Infections ◽  
Yellow Mosaic Virus ◽  
Protein Database ◽  
Dna Virus ◽  
Field Production

Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases.

scholarly journals A comprehensive and scalable database search system for metaproteomics

2016 ◽  
Author(s):  
Sandip Chatterjee ◽  
Gregory S. Stupp ◽  
Sung Kyu (Robin) Park ◽  
Jean-Christophe Ducom ◽  
John R. Yates ◽  
...  
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
High Throughput Sequencing ◽  
Shotgun Proteomics ◽  
Identification Accuracy ◽  
Sequencing Data ◽  
Protein Database ◽  
Healthy Human ◽  
Genomic Libraries ◽  
Sequence Databases

AbstractBackgroundMass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations.ResultsOur approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed “Blazmass”) to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy, and allowing for a more in-depth characterization of the functional landscape of the samples.ConclusionsThe combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomics search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

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