The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

https://cyberleninka.org/article/n/132565.pdf

Discovery and resupply of pharmacologically active plant-derived natural products: A review.

Biome-scaledisturbancesbyeruptiveherbivoresprovidevaluableinsightsintospeciesinteractions,ecosystemfunction,andimpactsof globalchange. We present a conceptual framework using one system as a model, emphasizing interactions across levels of biological hierarchy and spatiotemporal scales. Bark beetles are major natural disturbance agents in western North American forests. However, recent bark beetle population eruptions have exceeded the frequencies, impacts, and ranges documented during the previous 125 years. Extensive host abundance and susceptibility, concentrated beetle density, favorable weather, optimal symbiotic associations, and escape from natural enemies must occur jointly for beetles to surpass a series of thresholds and exert widespread disturbance. Opposing feedbacks determine qualitatively distinct outcomes at junctures at the biochemical through landscape levels. Eruptions occur when key thresholds are surpassed, prior constraints cease to exert influence, and positive feedbacks amplify across scales. These dynamics are bidirectional, as landscape features influence how lower-scale processes are amplified or buffered. Climate change and reduced habitat heterogeneity increase the likelihood that key thresholds will be exceeded, and may cause fundamental regime shifts. Systems in which endogenous feedbacks can dominate after external forces foster the initial breach of thresholds appear particularly sensitive to anthropogenic perturbations.

/pdf/cross-scale-drivers-of-natural-disturbances-prone-to-2h7fbj430j.pdf

Cross-scale Drivers of Natural Disturbances Prone to Anthropogenic Amplification: The Dynamics of Bark Beetle Eruptions

Plants respond to herbivory through various morphological, biochemicals, and molecular mechanisms to counter/offset the effects of herbivore attack. The biochemical mechanisms of defense against the herbivores are wide-ranging, highly dynamic, and are mediated both by direct and indirect defenses. The defensive compounds are either produced constitutively or in response to plant damage, and affect feeding, growth, and survival of herbivores. In addition, plants also release volatile organic compounds that attract the natural enemies of the herbivores. These strategies either act independently or in conjunction with each other. However, our understanding of these defensive mechanisms is still limited. Induced resistance could be exploited as an important tool for the pest management to minimize the amounts of insecticides used for pest control. Host plant resistance to insects, particularly, induced resistance, can also be manipulated with the use of chemical elicitors of secondary metabolites, which confer resistance to insects. By understanding the mechanisms of induced resistance, we can predict the herbivores that are likely to be affected by induced responses. The elicitors of induced responses can be sprayed on crop plants to build up the natural defense system against damage caused by herbivores. The induced responses can also be engineered genetically, so that the defensive compounds are constitutively produced in plants against are challenged by the herbivory. Induced resistance can be exploited for developing crop cultivars, which readily produce the inducible response upon mild infestation, and can act as one of components of integrated pest management for sustainable crop production.

https://www.tandfonline.com/doi/pdf/10.4161/psb.21663

Mechanisms of plant defense against insect herbivores

Contents

 Summary 657

I. Introduction 658
II. Identification and functional characterization of  terpenoid pathway genes 658
III. Insect interactions with conifers 667
IV. Conclusions and outlook 670

 Acknowledgements 671


 References 671



Summary
Insects select their hosts, but trees cannot select which herbivores will feed upon them. Thus, as long-lived stationary organisms, conifers must resist the onslaught of varying and multiple attackers over their lifetime. Arguably, the greatest threats to conifers are herbivorous insects and their associated pathogens. Insects such as bark beetles, stem- and wood-boring insects, shoot-feeding weevils, and foliage-feeding budworms and sawflies are among the most devastating pests of conifer forests. Conifer trees produce a great diversity of compounds, such as an enormous array of terpenoids and phenolics, that may impart resistance to a variety of herbivores and microorganisms. Insects have evolved to specialize in resistance to these chemicals – choosing, feeding upon, and colonizing hosts they perceive to be best suited to reproduction. This review focuses on the plant–insect interactions mediated by conifer-produced terpenoids. To understand the role of terpenoids in conifer–insect interactions, we must understand how conifers produce the wide diversity of terpenoids, as well as understand how these specific compounds affect insect behaviour and physiology. This review examines what chemicals are produced, the genes and proteins involved in their biosynthesis, how they work, and how they are regulated. It also examines how insects and their associated pathogens interact with, elicit, and are affected by conifer-produced terpenoids.

/pdf/genes-enzymes-and-chemicals-of-terpenoid-diversity-in-the-156bm97ppc.pdf

Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens.

Terpenoid biomaterials

White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.

Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.

Contact: [email protected]

Supplementary information:Supplementary data are available at Bioinformatics online.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

We report results that address a long-standing controversy in honey bee biology, the identity of the queen-produced compounds that inhibit worker honey bee ovary development. As the honey bee is the only organism for which identities have been proposed for any pheromone that regulates reproduction, the resolution of its identity is of broad significance. We examined the effects of synthetic honey bee queen mandibular pheromone (QMP), four newly identified queen retinue pheromone components, and whole-queen extracts on the ovary development of caged worker bees. The newly identified compounds did not inhibit worker ovary development alone, nor did they improve the efficacy of QMP when applied in combination. QMP was as effective as queen extracts at ovary regulation. Caged workers in the QMP and queen extract treatments had better developed ovaries than did workers remaining in queenright colonies. We conclude that QMP is responsible for the ovary-regulating pheromonal capability of queens from European-derived Apis mellifera subspecies.

Christopher I. Keeling

Papers

Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens.

Terpenoid biomaterials

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

The effect of queen pheromones on worker honey bee ovary development.

Diterpene resin acids in conifers.