scholarly journals Illuminating the plant rhabdovirus landscape through metatranscriptomics data

2021 ◽  
Author(s):  
nicolas bejerman ◽  
Ralf 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 26 novel rhabdovirus genomes associated with 24 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant and insect transcriptomes from the NCBI Sequence Read Archive (SRA) using known plant rhabdovirus sequences as query. 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 six 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 provides additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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.

scholarly journals Exploring the tymovirids landscape through metatranscriptomics data

2021 ◽  
Author(s):  
Nicolas Bejerman ◽  
Humberto Debat
Keyword(s):  
High Throughput Sequencing ◽  
The Novel ◽  
Virus Taxonomy ◽  
Coding Regions ◽  
Sequence Read Archive ◽  
Public Data ◽  
Positive Sense ◽  
Invaluable Tool ◽  
Sequencing Platforms ◽  
Viral Sequences

Tymovirales is an order of viruses with positive-sense, single-stranded RNA genomes that mostly infect plants, but also fungi and insects. The number of tymovirid sequences has been growing in the last few years with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 31 novel tymovirid genomes associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through a homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirids sequences as query. Identification, assembly and curation of raw SRA reads resulted in 29 viral genome sequences with full-length coding regions, and two partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known tymovirids. Phylogenetic analysis showed that six of the novel viruses were related to alphaflexiviruses, seventeen to betaflexiviruses, two to deltaflexiviruses and six to tymoviruses. These findings resulted in the most complete phylogeny of tymovirids to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and diversity of tymovirids genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.

scholarly journals Discovery and initial analysis of novel viral genomes in the soybean cyst nematode

2011 ◽  
Vol 92 (8) ◽  
pp. 1870-1879 ◽  
Author(s):  
Sadia Bekal ◽  
Leslie L. Domier ◽  
Terry L. Niblack ◽  
Kris N. Lambert
Keyword(s):  
Soybean Cyst Nematode ◽  
High Throughput Sequencing ◽  
Nematode Species ◽  
Cyst Nematode ◽  
Parasitic Nematodes ◽  
The Novel ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Virus Genomes ◽  
Viral Sequences

Nematodes are the most abundant multicellular animals on earth, yet little is known about their natural viral pathogens. To date, only two nematode virus genomes have been reported. Consequently, nematode viruses have been overlooked as important biotic factors in the study of nematode ecology. Here, we show that one plant parasitic nematode species, Heterodera glycines, the soybean cyst nematode (SCN), harbours four different RNA viruses. The nematode virus genomes were discovered in the SCN transcriptome after high-throughput sequencing and assembly. All four viruses have negative-sense RNA genomes, and are distantly related to nyaviruses and bornaviruses, rhabdoviruses, bunyaviruses and tenuiviruses. Some members of these families replicate in and are vectored by insects, and can cause significant diseases in animals and plants. The novel viral sequences were detected in both eggs and the second juvenile stage of SCN, suggesting that these viruses are transmitted vertically. While there was no evidence of integration of viral sequences into the nematode genome, we indeed detected transcripts from these viruses by using quantitative PCR. These data are the first finding of virus genomes in parasitic nematodes. This discovery highlights the need for further exploration for nematode viruses in all tropic groups of these diverse and abundant animals, to determine how the presence of these viruses affects the fitness of the nematode, strategies of viral transmission and mechanisms of viral pathogenesis.

scholarly journals High Throughput Nanopore Sequencing of SARS-CoV-2 Viral Genomes from Patient Samples

2021 ◽  
Author(s):  
Adrian A. Pater ◽  
Michael S. Bosmeny ◽  
Mansi Parasrampuria ◽  
Seth B. Eddington ◽  
Katy N. Ovington ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rna Extraction ◽  
Nanopore Sequencing ◽  
The Novel ◽  
Viral Genomes ◽  
Primer Sets ◽  
Novel Coronavirus ◽  
Sequencing Platforms ◽  
Effective Public Health

ABSTRACTIn late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking movement and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using online visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable ‘how-to’ reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and next-generation nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.

scholarly journals Virus Surveys in Olive Orchards in Greece Identify Olive Virus T, a Novel Member of the Genus Tepovirus

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 574
Author(s):  
Evanthia Xylogianni ◽  
Paolo Margaria ◽  
Dennis Knierim ◽  
Kyriaki Sareli ◽  
Stephan Winter ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Leaf Roll ◽  
Virus Infections ◽  
Northern Greece ◽  
Coat Protein Region ◽  
Cherry Leaf Roll Virus ◽  
Leaf Yellowing ◽  
Olive Trees ◽  
Olive Varieties ◽  
Viral Sequences

Field surveys were conducted in Greek olive orchards from 2017 to 2020 to collect information on the sanitary status of the trees. Using a high-throughput sequencing approach, viral sequences were identified in total RNA extracts from several trees and assembled to reconstruct the complete genomes of two isolates of a new viral species of the genus Tepovirus (Betaflexiviridae), for which the name olive virus T (OlVT) is proposed. A reverse transcription–polymerase chain reaction assay was developed which detected OlVT in samples collected in olive growing regions in Central and Northern Greece, showing a virus prevalence of 4.4% in the olive trees screened. Sequences of amplified fragments from the movement–coat protein region of OlVT isolates varied from 75.64% to 99.35%. Three olive varieties (Koroneiki, Arbequina and Frantoio) were infected with OlVT via grafting to confirm a graft-transmissible agent, but virus infections remained latent. In addition, cucumber mosaic virus, olive leaf yellowing-associated virus and cherry leaf roll virus were identified.

scholarly journals Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data

2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Yuhua Fu ◽  
Pengyu Fan ◽  
Lu Wang ◽  
Ziqiang Shu ◽  
Shilin Zhu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Target Prediction ◽  
Large Data ◽  
Sequencing Data ◽  
Regulate Gene Expression ◽  
High Throughput Sequencing Data ◽  
Annotation Information ◽  
Public Data ◽  
Broad Variety

Abstract Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.

scholarly journals Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions

2021 ◽  
Author(s):  
Mathilde Borg Dahl ◽  
Derek Peršoh ◽  
Anke Jentsch ◽  
Jürgen Kreyling
Keyword(s):  
Soil Temperature ◽  
Plant Species ◽  
High Throughput Sequencing ◽  
Calluna Vulgaris ◽  
Absolute Temperature ◽  
Snow Accumulation ◽  
Temperature Variability ◽  
Holcus Lanatus ◽  
Soil Frost ◽  
Winter Climate

AbstractWinter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.

scholarly journals Targeted sequencing and integrative analysis to prioritize candidate genes in neurodevelopmental disorders

2021 ◽  
Author(s):  
Yi Zhang ◽  
Tao Wang ◽  
Yan Wang ◽  
Kun Xia ◽  
Jinchen Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Neurodevelopmental Disorders ◽  
De Novo ◽  
Genetic Data ◽  
Chinese Patients ◽  
The Novel ◽  
Mutational Spectrum ◽  
Functional Variants ◽  
Public Data ◽  
Chromosomal Genes

AbstractNeurodevelopmental disorders (NDDs) are a group of diseases characterized by high heterogeneity and frequently co-occurring symptoms. The mutational spectrum in patients with NDDs is largely incomplete. Here, we sequenced 547 genes from 1102 patients with NDDs and validated 1271 potential functional variants, including 108 de novo variants (DNVs) in 78 autosomal genes and seven inherited hemizygous variants in six X chromosomal genes. Notably, 36 of these 78 genes are the first to be reported in Chinese patients with NDDs. By integrating our genetic data with public data, we prioritized 212 NDD candidate genes with FDR < 0.1, including 17 novel genes. The novel candidate genes interacted or were co-expressed with known candidate genes, forming a functional network involved in known pathways. We highlighted MSL2, which carried two de novo protein-truncating variants (p.L192Vfs*3 and p.S486Ifs*11) and was frequently connected with known candidate genes. This study provides the mutational spectrum of NDDs in China and prioritizes 212 NDD candidate genes for further functional validation and genetic counseling.

scholarly journals Identification of New, Functionally Relevant Mutations in the Coding Regions of the Human Fos and Jun Proto-Oncogenes in Rheumatoid Arthritis Synovial Tissue

Life ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 5
Author(s):  
René Huber ◽  
Sandra Augsten ◽  
Holger Kirsten ◽  
Roland Zell ◽  
Axel Stelzner ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Joint Inflammation ◽  
Germline Mutations ◽  
The Novel ◽  
Coding Regions ◽  
Cleavage Assay ◽  
Inflammatory Proteins ◽  
Functional Relevance ◽  
Nih 3T3 ◽  
Synovial Membranes

In rheumatoid arthritis (RA), the expression of many pro-destructive/pro-inflammatory proteins depends on the transcription factor AP-1. Therefore, our aim was to analyze the presence and functional relevance of mutations in the coding regions of the AP-1 subunits of the fos and jun family in peripheral blood (PB) and synovial membranes (SM) of RA and osteoarthritis patients (OA, disease control), as well as normal controls (NC). Using the non-isotopic RNAse cleavage assay, one known polymorphism (T252C: silent; rs1046117; present in RA, OA, and NC) and three novel germline mutations of the cfos gene were detected: (i) C361G/A367G: Gln121Glu/Ile123Val, denoted as “fos121/123”; present only in one OA sample; (ii) G374A: Arg125Lys, “fos125”; and (iii) C217A/G374A: Leu73Met/Arg125Lys, “fos73/125”, the latter two exclusively present in RA. In addition, three novel somatic cjun mutations (604–606ΔCAG: ΔGln202, “jun202”; C706T: Pro236Ser, “jun236”; G750A: silent) were found exclusively in the RA SM. Tansgenic expression of fos125 and fos73/125 mutants in NIH-3T3 cells induced an activation of reporter constructs containing either the MMP-1 (matrix metalloproteinase) promoter (3- and 4-fold, respectively) or a pentameric AP-1 site (approximately 5-fold). Combined expression of these two cfos mutants with cjun wildtype or mutants (jun202, jun236) further enhanced reporter expression of the pentameric AP-1 construct. Finally, genotyping for the novel functionally relevant germline mutations in 298 RA, 288 OA, and 484 NC samples revealed no association with RA. Thus, functional cfos/cjun mutants may contribute to local joint inflammation/destruction in selected patients with RA by altering the transactivation capacity of AP-1 complexes.

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