scholarly journals Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wentao Ye ◽  
Wei Xu ◽  
Nan Xu ◽  
Rong Chen ◽  
Changhu Lu ◽  
...  
Keyword(s):  
Transcriptional Regulatory Network ◽  
Full Length ◽  
Sequencing Data ◽  
Consensus Sequences ◽  
Grus Japonensis ◽  
Transcriptional Regulatory ◽  
Illumina Data ◽  
Transmission Pathways ◽  
First Time

AbstractThe red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. Here, we sequenced for the first time the full-length unreferenced transcriptome of red-crowned crane mixed samples using a PacBio Sequel platform. A total of 359,136 circular consensus sequences (CCS) were obtained via clustering to remove redundancy. A total of 303,544 full-length non-chimeric sequences were identified by judging whether CCS contained 5′ and 3′ adapters, and the poly(A) tail. Eight samples were sequenced using Illumina, and PacBio sequencing data were corrected according to the collected Illumina data to obtain more accurate full-length transcripts. A total of 4,100 long non-coding RNAs, 13,115 simple sequences repeat loci and 29 transcription factor families were identified. The expression of lncRNAs and TFs in pancreas was lowest comparing with other tissues. Many enriched immune-related transmission pathways (MHC and IL receptors) were identified in the spleen. This study will contribute to a better understanding of the gene structure and post-transcriptional regulatory network, and provide references for future studies on red-crowned cranes.

CHARACTERIZATION OF THE SPLICE SITES IN GT–AG AND GC–AG INTRONS IN HIGHER EUKARYOTES USING FULL-LENGTH cDNAs

2004 ◽  
Vol 02 (02) ◽  
pp. 309-331 ◽  
Author(s):  
SUMIE KITAMURA–ABE ◽  
HITOMI ITOH ◽  
TAKANORI WASHIO ◽  
AKIHIRO TSUTSUMI ◽  
MASARU TOMITA
Keyword(s):  
Alternative Splice ◽  
Splice Site ◽  
Consensus Sequence ◽  
Full Length ◽  
Splice Sites ◽  
Consensus Sequences ◽  
Full Length Cdna ◽  
Strong Consensus ◽  
Higher Eukaryotes

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT–AG and GC–AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT–AG and GC–AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC–AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.

scholarly journals Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle

2004 ◽  
Vol 20 (12) ◽  
pp. 1914-1927 ◽  
Author(s):  
H.-C. Chen ◽  
H.-C. Lee ◽  
T.-Y. Lin ◽  
W.-H. Li ◽  
B.-S. Chen
Keyword(s):  
Cell Cycle ◽  
Yeast Cell ◽  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Yeast Cell Cycle ◽  
Quantitative Characterization ◽  
Transcriptional Regulatory

scholarly journals Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 202 ◽  
Author(s):  
Verónica A. Bornancini ◽  
José M. Irazoqui ◽  
Ceferino R. Flores ◽  
Carlos G. Vaghi Medina ◽  
Ariel F. Amadio ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Full Length ◽  
Yellow Spot ◽  
Streak Virus ◽  
Rolling Circle ◽  
Viral Particles ◽  
Bipartite Genome ◽  
First Time ◽  
Leaf Virus

In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination.

scholarly journals isoformant: A visual toolkit for reference-free long-read isoform analysis at single-read resolution

2021 ◽  
Author(s):  
Daniel D Le ◽  
Faye T Orcales ◽  
William Stephenson
Keyword(s):  
Region Of Interest ◽  
Sequencing Data ◽  
Consensus Sequences ◽  
Interactive Analysis ◽  
Isoform Diversity ◽  
Oxford Nanopore ◽  
Long Read ◽  
Multiple Samples ◽  
Read Distribution

isoformant is an analytical toolkit for isoform characterization of Oxford Nanopore Technologies (ONT) long-transcript sequencing data (i.e. direct RNA and cDNA). Deployment of these tools using Jupyter Notebook enables interactive analysis of user- defined region-of-interest (ROI), typically a gene. The core module of isoformant clus- ters sequencing reads by k-mer density to generate isoform consensus sequences without the requirement for a reference genome or prior annotations. The inclusion of differential isoform usage hypothesis testing based on read distribution among clusters enables com- parison across multiple samples. Here, as proof-of-principle, we demonstrate the utility of isoformant for analyzing isoform diversity of commercially-available isoform standard mixtures. isoformant is available here: https://github.com/danledinh/isoformant.

scholarly journals Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization

2016 ◽  
Vol 62 (12) ◽  
pp. 1630-1638 ◽  
Author(s):  
Peter M Clark ◽  
Jamie L Duke ◽  
Deborah Ferriola ◽  
Valia Bravo-Egana ◽  
Tunde Vago ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Human Leukocyte ◽  
Full Length ◽  
Class I ◽  
Hla Alleles ◽  
Consensus Sequences ◽  
Leukocyte Antigen ◽  
Novel Alleles ◽  
Full Length Gene

Abstract BACKGROUND Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs. METHODS We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased full-length gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline. RESULTS Our analysis revealed that 7.7% (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated full-length gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles. CONCLUSIONS The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.

scholarly journals Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

2015 ◽  
Author(s):  
Jenny Chen ◽  
Alexander A. Shishkin ◽  
Xiaopeng Zhu ◽  
Sabah Kadri ◽  
Itay Maza ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
De Novo ◽  
Functional Characterization ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Evolutionary Analysis ◽  
Sequencing Data ◽  
Manual Curation ◽  
First Time

BACKGROUND: Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across multitudes of species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: 1) identifying truly noncoding genes from de novo reconstructed transcriptomes, and 2) prioritizing hundreds of resulting putative lncRNAs from each sample for downstream experimental interrogation. RESULTS: We present slncky, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-Sequencing data and further prioritizes lncRNAs by characterizing selective constraint as a proxy for function. Our filtering pipeline is comparable to manual curation efforts and more sensitive than previously published approaches. Further, we develop, for the first time, a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for both sequence and transcript evolution. Our analysis reveals that selection acts in several distinct patterns, and uncovers two notable classes of lncRNAs: one showing strong purifying selection at RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript. CONCLUSION: Our novel comparative methods for lncRNAs reveals 233 constrained lncRNAs out of tens of thousands of currently annotated transcripts, which we believe should be prioritized for further interrogation. To aid in their analysis we provide the slncky Evolution Browser as a resource for experimentalists.

TBE in Sweden

2020 ◽  
Keyword(s):  
Genetic Characterization ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Second Phase ◽  
Serum Samples ◽  
Tick Borne Encephalitis ◽  
Specific Immunoglobulin ◽  
Tick Borne Encephalitis Virus ◽  
First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

Chemical Constituents and Antibacterial Activity of Cissus Aralioides.

2020 ◽  
Vol 17 ◽  
Author(s):  
Balogun Olaoye Solomon ◽  
Ajayi Olukayode Solomon ◽  
Owolabi Temitayo Abidemi ◽  
Oladimeji Abdulkarbir Oladele ◽  
Liu Zhiqiang
Keyword(s):  
Plant Extract ◽  
Chemical Constituents ◽  
Ethyl Acetate Fraction ◽  
Antibacterial Activities ◽  
Sub Saharan Africa ◽  
Chromatographic Purification ◽  
Whole Plant ◽  
Sub Saharan ◽  
First Time

: Cissus aralioides is a medicinal plant used in sub-Saharan Africa for treatment of infectious diseases; however the chemical constituents of the plant have not been investigated. Thus, in this study, attempt was made at identifying predominant phytochemical constituents of the plant through chromatographic purification and silylation of the plant extract, and subsequent characterization using spectroscopic and GC-MS techniques. The minimum inhibitory concentration (MICs) for the antibacterial activities of the plant extract, chromatographic fractions and isolated compounds were also examined. Chromatographic purification of the ethyl acetate fraction from the whole plant afforded three compounds: β-sitosterol (1), stigmasterol (2) and friedelin (3). The phytosterols (1 and 2) were obtained together as a mixture. The GC-MS analysis of silylated extract indicated alcohols, fatty acids and sugars as predominant classes, with composition of 24.62, 36.90 and 26.52% respectively. Results of MICs indicated that friedelin and other chromatographic fractions had values (0.0626-1.0 mg/mL) comparable with the standard antibiotics used. Characterization of natural products from C. aralioides is being reported for the first time in this study.

Sign in / Sign up

Export Citation Format

Share Document