scholarly journals Anvi’o: an advanced analysis and visualization platform for ‘omics data

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1319 ◽  
Author(s):  
A. Murat Eren ◽  
Özcan C. Esen ◽  
Christopher Quince ◽  
Joseph H. Vineis ◽  
Hilary G. Morrison ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Complex Data ◽  
Omics Data ◽  
Multiple Sources ◽  
Genomic Changes ◽  
Naturally Occurring ◽  
Multiple Dimensions ◽  
Advanced Analysis

Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations throughde novocharacterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.

scholarly journals Anvi’o: An advanced analysis and visualization platform for ‘omics data

2015 ◽  
Author(s):  
A. Murat Eren ◽  
Özcan C Esen ◽  
Christopher Quince ◽  
Joseph H Vineis ◽  
Mitchell L Sogin ◽  
...  
Keyword(s):  
Time Series Data ◽  
De Novo ◽  
Draft Genome ◽  
Series Data ◽  
Omics Data ◽  
Modular Architecture ◽  
Sequence Contigs ◽  
Genomic Changes ◽  
Advanced Analysis ◽  
Functional Features

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi’o, an advanced analysis and visualization platform for ‘omics data, and its assembly-based metagenomic workflow. Anvi’o’s interactive interface facilitates the management of contigs and associated metadata for automatic or human-guided identification of genome bins, and their curation. Its extensible visualization approach distills multiple dimensions of information about each contig into a single, intuitive display, offering a dynamic and unified work environment for data exploration, manipulation and reporting. Beyond its easy-to-use interface, the advanced modular architecture of anvi’o as a platform allows users with programming skills to implement and test novel ideas with minimal effort. To demonstrate anvi’o’s capabilities, we re-analyzed a metagenomic time-series data from an infant gut microbiome. Through the anvi’o interface we identified near-complete draft genomes, and explored temporal genomic changes within the abundant microbial populations through de novo characterization of subtle nucleotide variations. We also used anvi’o to re-analyze a collection of datasets from multiple investigators who studied microbial responses to the Deepwater Horizon oil spill. We linked metagenomic, metatranscriptomic, and single-cell genomic data from the water plume, and used the holistic perspective anvi’o provides to identify the draft genome of a previously uncharacterized, active population of Oceanospirillales. We also linked environmental isolates with metagenomes recovered from an oil-contaminated beach, and identified 56 near-complete draft genomes including abundant oil degraders whose functional features suggested an oceanic origin.

scholarly journals Anvi’o: An advanced analysis and visualization platform for ‘omics data

2015 ◽  
Author(s):  
A. Murat Eren ◽  
Özcan C Esen ◽  
Christopher Quince ◽  
Joseph H Vineis ◽  
Mitchell L Sogin ◽  
...  
Keyword(s):  
Time Series Data ◽  
De Novo ◽  
Draft Genome ◽  
Series Data ◽  
Omics Data ◽  
Modular Architecture ◽  
Sequence Contigs ◽  
Genomic Changes ◽  
Advanced Analysis ◽  
Functional Features

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi’o, an advanced analysis and visualization platform for ‘omics data, and its assembly-based metagenomic workflow. Anvi’o’s interactive interface facilitates the management of contigs and associated metadata for automatic or human-guided identification of genome bins, and their curation. Its extensible visualization approach distills multiple dimensions of information about each contig into a single, intuitive display, offering a dynamic and unified work environment for data exploration, manipulation and reporting. Beyond its easy-to-use interface, the advanced modular architecture of anvi’o as a platform allows users with programming skills to implement and test novel ideas with minimal effort. To demonstrate anvi’o’s capabilities, we re-analyzed a metagenomic time-series data from an infant gut microbiome. Through the anvi’o interface we identified near-complete draft genomes, and explored temporal genomic changes within the abundant microbial populations through de novo characterization of subtle nucleotide variations. We also used anvi’o to re-analyze a collection of datasets from multiple investigators who studied microbial responses to the Deepwater Horizon oil spill. We linked metagenomic, metatranscriptomic, and single-cell genomic data from the water plume, and used the holistic perspective anvi’o provides to identify the draft genome of a previously uncharacterized, active population of Oceanospirillales. We also linked environmental isolates with metagenomes recovered from an oil-contaminated beach, and identified 56 near-complete draft genomes including abundant oil degraders whose functional features suggested an oceanic origin.

scholarly journals Home-made enzymatic premix and Illumina sequencing allow for one-step Gibson assembly and verification of virus infectious clones

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Mingmin Zhao ◽  
Beatriz García ◽  
Araiz Gallo ◽  
Ioannis E. Tzanetakis ◽  
Carmen Simón-Mateo ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Rna Virus ◽  
Infectious Clone ◽  
Gibson Assembly ◽  
Infectious Clones ◽  
Universal Approach ◽  
One Step ◽  
Step Generation

AbstractAn unprecedented number of viruses have been discovered by leveraging advances in high-throughput sequencing. Infectious clone technology is a universal approach that facilitates the study of biology and role in disease of viruses. In recent years homology-based cloning methods such as Gibson assembly have been used to generate virus infectious clones. We detail herein the preparation of home-made cloning materials for Gibson assembly. The home-made materials were used in one-step generation of the infectious cDNA clone of a plant RNA virus into a T-DNA binary vector. The clone was verified by a single Illumina reaction and a de novo read assembly approach that required no primer walking, custom primers or reference sequences. Clone infectivity was finally confirmed by Agrobacterium-mediated delivery to host plants. We anticipate that the convenient home-made materials, one-step cloning and Illumina verification strategies described herein will accelerate characterization of viruses and their role in disease development.

scholarly journals STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

2018 ◽  
Author(s):  
Huidong Chen ◽  
Luca Albergante ◽  
Jonathan Y Hsu ◽  
Caleb A Lareau ◽  
Giosue` Lo Bosco ◽  
...  
Keyword(s):  
Single Cell ◽  
De Novo ◽  
Developmental Trajectories ◽  
Cellular Heterogeneity ◽  
State Transitions ◽  
Omics Data ◽  
Transcriptomic Data ◽  
Lineage Differentiation ◽  
Cell Trajectories

AbstractSingle-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.

scholarly journals Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera

2020 ◽  
Vol 10 (10) ◽  
pp. 3843-3857
Author(s):  
Kira A. Treibergs ◽  
Gonzalo Giribet
Keyword(s):  
Gene Expression ◽  
Division Of Labor ◽  
Differential Gene Expression ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cdna Libraries ◽  
Living Species ◽  
Differential Gene

Bryozoans are a diverse phylum of marine and freshwater colonial invertebrates containing approximately 6,300 described living species. Bryozoans grow by budding new physiologically connected colony members (zooids) from a founding individual that forms from a metamorphosed larva. In some species these zooids come in different shapes and sizes and are specialized to serve different tasks within the colony. A complex interaction of genotype, environment, and developmental pathway shapes zooid fate, however, the specific mechanisms underlying the establishment of this division of labor remain unknown. Here, the first characterization of differential gene expression between polymorphic zooids of a bryozoan colony is presented. The development of different zooid types of lab-cultured Bugulina stolonifera colonies including feeding autozooids, avicularia (derived non-feeding zooids that are homologous to feeding autozooids but shaped like a bird’s beak), and rhizoids (a branching network of non-feeding anchoring zooids) was explored using RNA sequencing, de novo transcriptome assembly, and differential gene expression analyses. High throughput sequencing of cDNA libraries yielded an average of 14.9 ± 1.3 (SE) million high-quality paired-end reads per sample. Data for the first de novo transcriptome assemblies of B. stolonifera and the first characterization of genes involved in the formation and maintenance of zooid types within a bryozoan colony are presented. In a comparison between autozooid and avicularium tissues, 1,097 significant differentially expressed genes were uncovered. This work provides a much-needed foundation for understanding the mechanisms involved in the development of polymorphic zooids and the establishment of division of labor in bryozoans.

scholarly journals De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Bhaskar Reddy ◽  
Amrutlal K. Patel ◽  
Krishna M. Singh ◽  
Deepak B. Patil ◽  
Pinesh V. Parikh ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Open Reading Frames ◽  
Dinucleotide Repeats ◽  
Kegg Pathways ◽  
Ion Torrent Pgm ◽  
Retinal Tissue ◽  
Retinol Metabolism ◽  
And Function

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.

scholarly journals High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Aderito Tomàs Pais da Cunha ◽  
Michela Chiumenti ◽  
Laurindo Chambula Ladeira ◽  
Raied Abou Kubaa ◽  
Giuliana Loconsole ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Rna Seq ◽  
Citrus Industry ◽  
Certification Programs ◽  
Molecular Variants ◽  
Pooled Samples ◽  
Tristeza Virus

Abstract Background Citrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries, which could act as diversity hotspots for CTV. Early detection and characterization of dangerous or emerging strains of this virus greatly help to prevent outbreaks of disease. This is particularly relevant in those growing regions where no dedicated certification programs are currently in use. Methods Double-stranded RNA extracted from Citrus spp. samples, collected in two locations in Angola, were pooled and submitted to a random-primed RNA-seq. This technique was performed to acquire a higher amount of data in the survey, before the amplification and sequencing of genes from single plants. To confirm the CTV infection in individual plants, as suggested by RNA-seq information from the pooled samples, the analysis was integrated with multiple molecular marker amplification (MMM) for the main known CTV strains (T30, T36, VT and T3). Results From the analysis of HTS data, several assembled contigs were identified as CTV and classified according to their similarity to the established strains. By the MMM amplification, only five individual accessions out of the eleven pooled samples, resulted to be infected by CTV. Amplified coat protein genes from the five positive sources were cloned and sequenced and submitted to phylogenetic analysis, while a near-complete CTV genome was also reconstructed by the fusion of three overlapping contigs. Conclusion Phylogenetic analysis of the ORF1b and CP genes, retrieved by de novo assembly and RT-PCR, respectively, revealed the presence of a wide array of CTV strains in the surveyed citrus-growing spots in Angola. Importantly, molecular variants among those identified from HTS showed high similarity with known severe strains as well as to recently described and emerging strains in other citrus-growing regions, such as S1 (California) or New Clade (Uruguay).

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

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