scholarly journals Genetic diversity of novel circular ssDNA viruses in bats in China

2011 ◽  
Vol 92 (11) ◽  
pp. 2646-2653 ◽  
Author(s):  
Xingyi Ge ◽  
Jialu Li ◽  
Cheng Peng ◽  
Lijun Wu ◽  
Xinglou Yang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Full Length ◽  
Inverse Pcr ◽  
Sequencing Data ◽  
Stem Loop ◽  
Amplification Method ◽  
Loop Region ◽  
The Family ◽  
Circular Ssdna ◽  
Ssdna Viruses

Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem–loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.

scholarly journals Comparative Transcriptome Profiling Analysis to Unravel the Potential Mechanism of Seed Abortion in Lumnitzera littorea

2021 ◽  
Vol 25 (02) ◽  
pp. 420-426
Author(s):  
Jingwen Zhang
Keyword(s):  
High Throughput Sequencing ◽  
Transcriptome Profiling ◽  
Seed Abortion ◽  
Sequencing Data ◽  
Mangrove Plant ◽  
Kegg Pathways ◽  
High Throughput Sequencing Data ◽  
Natural Reproduction ◽  
The Family ◽  
Profiling Analysis

Lumnitzera littorea (Jack) Voigt. is a species of mangrove plant belonging to the family Combretaceae. Natural reproduction of L. littorea is extremely difficult due to its seed abortion in China. To reveal the molecular mechanism of seed abortion, we performed transcriptome to analyze the seeds of L. littorea-T (normal seeds) and L. littorea-S (abortive seeds). After analysis of the raw data, 64,868 transcripts (mean length = 658 bp) were assembled. Among these transcripts, 39,779 were functionally annotated. Then, differentially expressed genes (DEGs) were screened, and 23,513 transcripts were identified that were likely involved in seed abortion. About 207 DEGs assigned to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and approximately 12.1% fell into reproduction categories. Genes involved in response to sucrose and starch metabolism, and phytohormone biosynthesis showed significant different expression levels between normal and abortive seeds of L. littorea. Further expressions patterns of key genes contribute to seed development were analyzed using quantitative real-time PCR, and the results were consistent with high-throughput sequencing data. The information obtained in this study will aid in the research of the mechanism of seed abortion in further molecular studies of L. littorea. © 2021 Friends Science Publishers

scholarly journals StoatyDive: Evaluation and Classification of Peak Profiles for Sequencing Data

2019 ◽  
Author(s):  
Florian Heyl ◽  
Rolf Backofen
Keyword(s):  
Quality Control ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Sequence Motif ◽  
Sequence Motifs ◽  
Sequencing Data ◽  
Stem Loop ◽  
Link Type ◽  
Quality Control Tool ◽  
Downstream Analysis

The prediction of binding sites (peak calling) is a common task in the data analysis of methods such as crosslinking or chromatin immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq, ChIP-Seq). The predicted binding sites are often further analyzed to predict sequence motifs or structure patterns as an example. However, the obtained peak set can vary in their profile shapes because of the used peakcaller method, different binding domains of the protein, protocol biases, or other factors. Thus, a tool is missing that evaluates and classifies the predicted peaks based on their shapes. We hereby present StoatyDive, a tool that can be used to filter for specific peak profile shapes of sequencing data such as CLIP and ChIP. StoatyDive therefore fine tunes downstream analysis steps such as structure or sequence motif predictions and acts as a quality control.With StoatyDive we were able to classify distinct peak profile shapes from CLIP-seq data of the histone stem-loop-binding protein (SLBP). We show the potential of StoatyDive, as a quality control tool and as a filter to pick different shapes based on biological or methodical questions.StoatyDive is open source and freely available under GLP-3 at https://github.com/BackofenLab/StoatyDive and at bioconda https://anaconda.org/bioconda/stoatydive.

scholarly journals A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Simon Haile ◽  
Richard D. Corbett ◽  
Veronique G. LeBlanc ◽  
Lisa Wei ◽  
Stephen Pleasance ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput Sequencing ◽  
Single Cells ◽  
Cell Types ◽  
Full Length ◽  
Sequencing Data ◽  
Total Rna ◽  
Specific Protocol

RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analyses at the single-cell level, allowing researchers to study heterogeneous mixtures of cells at unprecedented resolution. Tumors tend to be composed of heterogeneous cellular mixtures and are frequently the subjects of such analyses. Extensive method developments have led to several protocols for scRNAseq but, owing to the small amounts of RNA in single cells, technical constraints have required compromises. For example, the majority of scRNAseq methods are limited to sequencing only the 3′ or 5′ termini of transcripts. Other protocols that facilitate full-length transcript profiling tend to capture only polyadenylated mRNAs and are generally limited to processing only 96 cells at a time. Here, we address these limitations and present a novel protocol that allows for the high-throughput sequencing of full-length, total RNA at single-cell resolution. We demonstrate that our method produced strand-specific sequencing data for both polyadenylated and non-polyadenylated transcripts, enabled the profiling of transcript regions beyond only transcript termini, and yielded data rich enough to allow identification of cell types from heterogeneous biological samples.

A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

2021 ◽  
Vol 102 (12) ◽  
Author(s):  
Caroline Tochetto ◽  
Samuel Paulo Cibulski ◽  
Ana Paula Muterle Varela ◽  
Cristine Cerva ◽  
Diane Alves de Lima ◽  
...  
Keyword(s):  
Potential Role ◽  
Clinical Signs ◽  
Viral Metagenomics ◽  
Dna Viruses ◽  
Circular Dna ◽  
Viral Genomes ◽  
The Family ◽  
Circular Ssdna ◽  
Ssdna Viruses ◽  
Targeted Approach

Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named ‘Suismacovirus’, comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses’ genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.

scholarly journals Access COI barcode efficiently using high throughput Single-End 400 bp sequencing

2018 ◽  
Author(s):  
Chentao Yang ◽  
Shangjin Tan ◽  
Guangliang Meng ◽  
David G. Bourne ◽  
Paul A. O’Brien ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Full Length ◽  
List Type ◽  
Sequencing Data ◽  
Test Plate ◽  
Function Modules ◽  
Sequencing Platforms

SummaryOver the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, constraints in barcoding costs led to unbalanced efforts which prevented accurate taxonomic identification for biodiversity studies.We present a high throughput sequencing approach based on the HIFI-SE pipeline which takes advantage of Single-End 400 bp (SE400) sequencing data generated by BGISEQ-500 to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons. HIFI-SE was written in Python and included four function modules of filter, assign, assembly and taxonomy.We applied the HIFI-SE to a test plate which contained 96 samples (30 corals, 64 insects and 2 blank controls) and delivered a total of 86 fully assembled HIFI COI barcodes. By comparing to their corresponding Sanger sequences (72 sequences available), it showed that most of the samples (98.61%, 71/72) were correctly and accurately assembled, including 46 samples that had a similarity of 100% and 25 of ca. 99%.Our approach can produce standard full-length barcodes cost efficiently, allowing DNA barcoding for global biomes which will advance DNA-based species identification for various ecosystems and improve quarantine biosecurity efforts.

scholarly journals Date palm virus A: first plant virus found in date palm trees

2020 ◽  
Author(s):  
Ayoub Maachi ◽  
Tatsuya Nagata ◽  
João Marcos Fagundes Silva
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
Date Palm ◽  
Genomic Sequence ◽  
Triple Gene Block ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Sequencing Data ◽  
Novel Genus ◽  
The Family

AbstractIn this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2 and 3) and coat protein (CP). Phylogenetic analysis based on the Rep and the CP amino acid sequences showed the closest relationship to garlic yellow mosaic-associated virus (GYMaV). Based on the demarcation criteria of the family Betaflexiviridae, this new virus, provisionally named date palm virus A (DPVA), could constitute a member of a novel genus. However, considering that DPVA and GYMaV share the same genomic organization and that they cluster together on the Rep phylogenetic analysis, they could also constitute a novel genus together, highlighting the necessity of a revision of the taxonomic criteria of the family Betaflexiviridae.

scholarly journals A New World begomovirus infecting Grapevine

2020 ◽  
Author(s):  
Humberto Debat ◽  
Diego Zavallo ◽  
Sabrina Moyano ◽  
Facundo Luna ◽  
Sebastian Asurmendi ◽  
...  
Keyword(s):  
New World ◽  
High Throughput Sequencing ◽  
Bipartite Begomovirus ◽  
Agricultural Crop ◽  
Sequencing Data ◽  
Enveloped Viruses ◽  
High Throughput Sequencing Data ◽  
Circular Ssdna ◽  
Dna Components ◽  
Unassigned Species

AbstractGrapevine (Vitis L.), a deciduous woody vine, is a highly valuable agricultural crop. Grapevine, as other crops, is vulnerable to infectious pathogens. Several of them, including viruses, are a major threat to viticulture. Geminiviruses (family Geminiviridae) are insect transmitted, small non-enveloped viruses, with circular single-stranded DNA genomes, which are encapsidated in quasi-icosahedral geminated virions. There are only four geminiviruses associated to grapevine: two members of genus Grablovirus and two unassigned species. Here we present evidence of a novel begomovirus (genus Begomovirus) infecting grapevines from Argentina. Two circular ssDNA virus sequences were assembled from high-throughput sequencing data from Vitis vinifera cv Torrontes from Mendoza province, Argentina. Structural and functional annotation indicated that the virus sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, the first begomovirus reported to infect grapevine, a tentative prototype member of a novel species which we propose the name “grapevine begomovirus A” (GBVA).

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