The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.

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DeepMAsED: evaluating the quality of metagenomic assemblies

Bioinformatics ◽

10.1093/bioinformatics/btaa124 ◽

2020 ◽

Vol 36 (10) ◽

pp. 3011-3017 ◽

Cited By ~ 5

Author(s):

Olga Mineeva ◽

Mateo Rojas-Carulla ◽

Ruth E Ley ◽

Bernhard Schölkopf ◽

Nicholas D Youngblut

Keyword(s):

Large Scale ◽

State Of The Art ◽

Ground Truth ◽

Supplementary Information ◽

Learning Approach ◽

Wide Range ◽

Metagenome Assembly ◽

Model Training ◽

Reference Genomes

Abstract Motivation Methodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large-scale metagenome assemblies. Results We present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates a 1% contig misassembly rate in two recent large-scale metagenome assembly publications. Conclusions DeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modeling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects. Availability and implementation DeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED. Supplementary information Supplementary data are available at Bioinformatics online.

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Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

Genomics Insights ◽

10.4137/gei.s12732 ◽

2013 ◽

Vol 6 ◽

pp. GEI.S12732 ◽

Cited By ~ 6

Author(s):

Archana Sharma ◽

T. Satyanarayana

Keyword(s):

Comparative Genomics ◽

Molecular Biology ◽

Genome Sequencing ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Bacillus Species ◽

Genome Sequences ◽

Wide Range ◽

Sequencing Platforms ◽

Analytical Tools

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

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jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

10.1101/650747 ◽

2019 ◽

Author(s):

Lucas A. Nell

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Population Genomics ◽

R Package ◽

Gene Trees ◽

Sequencing Platform ◽

Genomic Variants ◽

Pacific Biosciences ◽

Wide Range ◽

Reference Genomes

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.

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DeepMAsED: Evaluating the quality of metagenomic assemblies

10.1101/763813 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mateo Rojas-Carulla ◽

Ruth E. Ley ◽

Bernhard Schölkopf ◽

Nicholas D. Youngblut

Keyword(s):

Large Scale ◽

State Of The Art ◽

Ground Truth ◽

Learning Approach ◽

Wide Range ◽

Metagenome Assembly ◽

Model Training ◽

Modelling Assumptions ◽

Reference Genomes

AbstractMotivation/backgroundMethodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large scale metagenome assemblies.ResultsWe present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates close to a 5% contig misassembly rate in two recent large-scale metagenome assembly publications.ConclusionsDeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modelling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects.AvailabilityDeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED.

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Advances in understanding the evolution of fungal genome architecture

F1000Research ◽

10.12688/f1000research.25424.1 ◽

2020 ◽

Vol 9 ◽

pp. 776 ◽

Cited By ~ 1

Author(s):

Shelby J. Priest ◽

Vikas Yadav ◽

Joseph Heitman

Keyword(s):

Large Scale ◽

High Throughput Sequencing ◽

Rapid Evolution ◽

Genomic Diversity ◽

Fungal Genome ◽

Small Scale ◽

Genomic Changes ◽

Wide Range ◽

Domains Of Life ◽

Fungal Genomes

Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.

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What is Bioinformatics? A Proposed Definition and Overview of the Field

Methods of Information in Medicine ◽

10.1055/s-0038-1634431 ◽

2001 ◽

Vol 40 (04) ◽

pp. 346-358 ◽

Cited By ~ 184

Author(s):

N. M. Luscombe ◽

D. Greenbaum ◽

M. Gerstein

Keyword(s):

Functional Genomics ◽

Computer Science ◽

Large Scale ◽

Structural Alignment ◽

Heterogeneous Data ◽

Computational Techniques ◽

Expression Data ◽

Genome Sequences ◽

Additional Information ◽

Wide Range

Summary Background: The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Objectives: Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Methods: Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying “informatics” techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Results and Conclusions: Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (eg expression data). Additional information includes the text of scientific papers and “relationship data” from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

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GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

10.1101/267393 ◽

2018 ◽

Cited By ~ 6

Author(s):

Danny E. Miller ◽

Cynthia Staber ◽

Julia Zeitlinger ◽

R. Scott Hawley

Keyword(s):

Single Molecule ◽

Drosophila Species ◽

High Quality ◽

Additional Species ◽

Oxford Nanopore ◽

Wide Range ◽

Long Read ◽

Genome Assemblies ◽

High Quality Genome ◽

Reference Genomes

ABSTRACTThe Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present high-quality genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.

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Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100131449 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1362-1363

Author(s):

V. C. Kannan ◽

A. K. Singh ◽

R. B. Irwin ◽

S. Chittipeddi ◽

F. D. Nkansah ◽

...

Keyword(s):

Integrated Circuits ◽

Large Scale ◽

Hexagonal Phase ◽

Microscopy Study ◽

Electron Microscopy Study ◽

Process Conditions ◽

Tin Films ◽

Wide Range ◽

Fcc Phase ◽

Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

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THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

Collection of scientific works of Odesa Military Academy ◽

10.37129/2313-7509.2019.11.53-58 ◽

2019 ◽

pp. 53-58

Author(s):

О. Кravchuk ◽

V. Symonenkov ◽

I. Symonenkova ◽

O. Hryhorev

Keyword(s):

Large Scale ◽

Armed Forces ◽

Distributed Information ◽

Wide Range ◽

Highly Effective ◽

Information Management Systems ◽

Robotic Devices ◽

Principles And Standards ◽

And Control ◽

The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

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Stirring and aeration system for the upgrading of small waste water treatment plants

Water Science & Technology ◽

10.2166/wst.1994.0600 ◽

1994 ◽

Vol 29 (12) ◽

pp. 149-156 ◽

Cited By ~ 4

Author(s):

Marcus Höfken ◽

Katharina Zähringer ◽

Franz Bischof

Keyword(s):

Waste Water ◽

Water Treatment ◽

Large Scale ◽

Waste Water Treatment ◽

Water Treatment Plants ◽

Waste Water Treatment Plants ◽

Basic Fluid ◽

Aeration System ◽

Technical Realization ◽

Wide Range

A novel agitating system has been developed which allows for individual or combined operation of stirring and aeration processes. Basic fluid mechanical considerations led to the innovative hyperboloid design of the stirrer body, which ensures high efficiencies in the stirring and the aeration mode, gentle circulation with low shear forces, excellent controllability, and a wide range of applications. This paper presents the basic considerations which led to the operating principle, the technical realization of the system and experimental results in a large-scale plant. The characteristics of the system and the differences to other stirring and aeration systems are illustrated. Details of the technical realization are shown, which conform to the specific demands of applications in the biological treatment of waste water. Special regard is given to applications in the upgrading of small compact waste water treatment plants.

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