scholarly journals Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

2020 ◽  
Author(s):  
Xiaofeng Xu ◽  
Jinlong Bei ◽  
Yibo Xuan ◽  
Jianyuan Chen ◽  
Defu Chen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Genome Sequence ◽  
Small Rna ◽  
Rna Virus ◽  
Phylogenetic Analyses ◽  
Full Length ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Link Type ◽  
Full Length Genome

AbstractIn 2014, A novel tick-borne virus of the genus Flavivirus was first reported from the Mogiana region in Brazil. This virus was named the Mogiana tick virus (MGTV). Later, MGTV was also named as Jingmen tick virus (JMTV), Kindia tick virus (KDTV), Guangxi tick virus (GXTV) etc. In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and detected MGTV in Amblyomma testudinarium ticks, which had been captured in Yunnan province of China in the year of 2016. The full-length genome sequence of a new MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) was obtained and recommended to be included into the NCBI RefSeq database for the future studies of MGTV. Our phylogenetic analyses showed that viruses named MGTV, JMTV, KDTV and GXTV are monophyletic: the MGTV group (lineage) of viruses. We show, for the first time, that 5′ and 3′ sRNAs can be used to obtain full-length sequences of the 5’ and 3’ ends of, but not limited to genome sequences of RNA viruses. And we proved the feasibility of using the sRNA-seq based method for the detection of viruses in a sample containing miniscule RNA.

scholarly journals Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaofeng Xu ◽  
Jinlong Bei ◽  
Yibo Xuan ◽  
Jiayuan Chen ◽  
Defu Chen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Genome Sequence ◽  
Small Rna ◽  
Rna Viruses ◽  
Rna Virus ◽  
Full Length ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Geographical Regions ◽  
Full Length Genome

Abstract Background In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

scholarly journals COMPASS: a COMprehensive Platform for smAll RNA-Seq data analySis

2019 ◽  
Author(s):  
Jiang Li ◽  
Alvin T. Kho ◽  
Robert P. Chase ◽  
Lorena Pantano-Rubino ◽  
Leanna Farnam ◽  
...  
Keyword(s):  
Data Analysis ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rnas ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Data Set ◽  
Sequence Processing ◽  
Rna Analysis ◽  
Link Type

AbstractBackgroundCirculating RNAs are potential disease biomarkers and their function is being actively investigated. Next generation sequencing (NGS) is a common means to interrogate the small RNA’ome or the full spectrum of small RNAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RNA’ome constituent components. Most existing NGS data analysis tools focus on the microRNA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RNA’ome, a prerequisite for down-stream data analysis.ResultsWe present COMPASS, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPASS contains prebuilt customizable standard RNA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPASS against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPASS identified a greater diversity and abundance of small RNA molecules.ConclusionCOMPASS is modular, stand-alone and integrates multiple customizable RNA databases and sequence processing tool and is distributed under the GNU General Public License free to non-commercial registered users at https://regepi.bwh.harvard.edu/circurna/ and the source code is available at https://github.com/cougarlj/COMPASS.

scholarly journals Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1110
Author(s):  
Aleš Eichmeier ◽  
Eliška Peňázová ◽  
Jana Čechová ◽  
Akila Berraf-Tebbal
Keyword(s):  
Vitis Vinifera ◽  
Rna Sequencing ◽  
Small Rna ◽  
Phylogenetic Analyses ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Hop Stunt Viroid ◽  
Grapevine Virus B ◽  
Grapevine Pinot Gris Virus ◽  
Rupestris Stem Pitting

Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.

scholarly journals Characterizing the cancer-associated microbiome with small RNA sequencing data

2020 ◽  
Vol 522 (3) ◽  
pp. 776-782
Author(s):  
Wei-Hao Lee ◽  
Kai-Pu Chen ◽  
Kai Wang ◽  
Hsuan-Cheng Huang ◽  
Hsueh-Fen Juan
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data

scholarly journals miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data

2016 ◽  
Vol 13 (5) ◽  
Author(s):  
Matthew Kanke ◽  
Jeanette Baran-Gale ◽  
Jonathan Villanueva ◽  
Praveen Sethupathy
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Cell Types ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Additional Information ◽  
Disease States ◽  
Non Coding Rnas ◽  
The Rich

SummarySmall non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the sequencing data to provide a comprehensive view of the microRNA landscape. Here we present miRquant 2.0, an expanded bioinformatics tool for accurate annotation and quantification of microRNAs and their isoforms (termed isomiRs) from small RNA-sequencing data. We anticipate that miRquant 2.0 will be useful for researchers interested not only in quantifying known microRNAs but also mining the rich well of additional information embedded in small RNA-sequencing data.

scholarly journals Evidence for human microRNA-offset RNAs in small RNA sequencing data

2009 ◽  
Vol 25 (18) ◽  
pp. 2298-2301 ◽  
Author(s):  
D. Langenberger ◽  
C. Bermudez-Santana ◽  
J. Hertel ◽  
S. Hoffmann ◽  
P. Khaitovich ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data

scholarly journals In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data

Genomics Data ◽  
2016 ◽  
Vol 7 ◽  
pp. 46-53 ◽  
Author(s):  
Suyash Agarwal ◽  
Naresh Sahebrao Nagpure ◽  
Prachi Srivastava ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
...  
Keyword(s):  
Pineal Gland ◽  
Rna Sequencing ◽  
Danio Rerio ◽  
Small Rna ◽  
In Silico ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Genome Wide ◽  
The Brain

Traces of post-transcriptional RNA modifications in deep sequencing data

2011 ◽  
Vol 392 (4) ◽  
Author(s):  
Sven Findeiß ◽  
David Langenberger ◽  
Peter F. Stadler ◽  
Steve Hoffmann
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Data Sets ◽  
Sequencing Data ◽  
Rna Modifications ◽  
Deep Sequencing Data ◽  
Complex Processes ◽  
Mature Micrornas ◽  
Rna Maturation

Abstract Many aspects of the RNA maturation leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes, in particular, genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in the form of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes. Here, we focus on small RNA sequencing data that is produced in large quantities aimed at the analysis of microRNA expression. Starting from the recovery of many well known modified sites in tRNAs, we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which surprisingly can be found in a diverse collection of transcripts including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.

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