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)

Half of all insect species are dependent on living plant tissues, consuming about 10% of plant annual production in natural habitats and an even greater percentage in agricultural systems, despite sophisticated control measures. Plants are generally remarkably well-protected against insect attack, with the result that most insects are highly specialized feeders. The mechanisms underlying plant resistance to invading herbivores on the one side, and insect food specialization on the other, are the main subjects of this book. For insects these include food-plant selection and the complex sensory processes involved, with their implications for learning and nutritional physiology, as well as the endocrinological spects of life cycle synchronization with host plant phenology. In the case of plants exposed to insect herbivores, they include the activation of defence systems in order to minimize damage, as well as the emission of chemical signals that may attract natural enemies of the invading herbivores and maybe exploited by neighbouring plants that mount defences as well.

Insect-plant biology

INTRODUCTION. Internal Organization of the Plant Body. Summary of Types of Cells and Tissues. General References. DEVELOPMENT OF THE SEED PLANT. The Embryo. From embryo to the Adult Plant. Apical Meristems and Their Derivatives. Differentiation, Specialization, and Morphogenesis. References. THE CELL. Cytoplasm. Nucleus. Plastids. Mitochondria. Microbodies. Vacuoles. Paramural Bodies. Ribosomes. Dictyosomes. Endoplasmic Reticulum. Lipid Globules. Microtubules. Ergastic Substances. References. CELL WALL. Macromolecular Components and Their Organization in the Wall. Cell Wall Layers. Intercellular Spaces. Pits, Primary Pit--Fields, and Plasmodesmata. Origin of Cell Wall During Cell Division. Growth of Cell Wall. References. PARENCHYMA AND COLLENCHYMA. Parenchyma. Collenchyma. References. SCLERENCHYMA. Sclereids. Fibers. Development of Sclereids and Fibers. References. EPIDERMIS. Composition. Developmental Aspects. Cell Wall. Stomata. Trichomes. References. XYLEM: GENERAL STRUCTURE AND CELL TYPES. Gross Structure of Secondary Xylem. Cell Types in the Secondary Xylem. Primary Xylem. Differentiation of Tracheary Elements. References. XYLEM: VARIATION IN WOOD STRUCTURE. Conifer Wood. Dicotyledon Wood. Some Factors in Development of Secondary Xylem. Identification of Wood. References. VASCULAR CAMBIUM. Organization of Cambium. Developmental Changes in the Initial Layer. Patterns and Causal Relations in Cambial Activity. References. PHLOEM. Cell Types. Primary Phloem. Secondary Phloem. References. PERIDERM. Structure of Periderm and Related Tissues. Development of Periderm. Outer Aspect of Bark in Relation to Structure. Lenticels. References. SECRETORY STRUCTURES. External Secretory Structures. Internal Secretory Structures. References. THE ROOT: PRIMARY STATE OF GROWTH. Types of Roots. Primary Structure. Development. References. THE ROOT: SECONDARY STATE OF GROWTH AND ADVENTITIOUS ROOTS. Common Types of Secondary Growth. Variations in Secondary Growths. Physiologic Aspects of Secondary Growth in Roots. Adventitious Roots. References. THE STEM: PRIMARY STATE OF GROWTH. External Morphology. Primary Structure. Development. References. THE STEM: SECONDARY GROWTH AND STRUCTURAL TYPES. Secondary Growth. Types of Stems. References. THE LEAF: BASIC STRUCTURE AND DEVELOPMENT. Morphology. Histology of Angiosperm Leaf. Development. Abscission. References. THE LEAF: VARIATIONS IN STRUCTURE. Leaf Structure and Environment. Dicotyledon Leaves. Monocotyledon Leaves. Gymnosperm Leaves. References. THE FLOWER: STRUCTURE AND DEVELOPMENT. Concept. Structure. Development. References. THE FLOWER: REPRODUCTIVE CYCLE. Microsporogenesis. Pollen. Male Gametophyte. Megasporogenesis. Female Gametophyte. Fertilization. References. THE FRUIT. Concept and Classification. The Fruit Wall. Fruit Types. Fruit Growths. Fruit Abscission. References. THE SEED. Concept and Morphology. Seed Development. Seed Coat. Nutrient Storage Tissues. References. EMBRYO AND SEEDLING. Mature Embryo. Development of Embryo. Classification of Embryos. Seedling. References. Glossary. Index.

Anatomy of Seed Plants

Biodiversity and Ecosystem Function

Managing metabolic resources is critical for insects during diapause when food sources are limited or unavailable. Insects accumulate reserves prior to diapause, and metabolic depression during diapause promotes reserve conservation. Sufficient reserves must be sequestered to both survive the diapause period and enable postdiapause development that may involve metabolically expensive functions such as metamorphosis or long-distance flight. Nutrient utilization during diapause is a dynamic process, and insects appear capable of sensing their energy reserves and using this information to regulate whether to enter diapause and how long to remain in diapause. Overwintering insects on a tight energy budget are likely to be especially vulnerable to increased temperatures associated with climate change. Molecular mechanisms involved in diapause nutrient regulation remain poorly known, but insulin signaling is likely a major player. We also discuss other possible candidates for diapause-associated nutrient regula...

Energetics of Insect Diapause

Galls of Diplolepis variabilis (Bassett) (Hymenoptera: Cynipidae) on their host plant Rosa woodsii Lindley (Rosaceae) support a diverse community of parasitoid and inquiline wasps that exploit the gall inducer and the gall itself. Here, we studied quantitative variation in local structure of the gall community in the Okanagan Valley of southern British Columbia, Canada, from the United States border north, to test the hypothesis that dispersal limitation would generate a distance decay in gall community similarity. We also explored gall community richness in relation to latitude, as the northern range limit of the gall inducer occurs within our study area. We found that gall communities exhibited strikingly similar composition across the study region, with most of the major inquilines and parasitoids present across the gall's range. However, the increased richness of rare parasitoid taxa near the northern range limits of D. variabilis generated a marginally significant positive relationship between gall community richness and latitude. Overall, our study suggests that dispersal constraints do not influence the composition of the Diplolepis Geoffroy gall community at regional scales, and that gall communities offer useful models for studying the association between community structure and range limits.

Variability in the parasitoid community associated with galls of Diplolepis variabilis (Hymenoptera: Cynipidae): a test of the distance decay hypothesis

Stems of Canada thistle ( Cirsium arvense (L.) Scop.), with galls of Urophora cardui (L.) at various stages of development, were brushed with a concentrated solution of dimefhoate to kill the gall-inducing larvae. Tissues of untreated and treated galls were compared to study the influence of larvae on each phase of gall growth and development. Galls treated in the initiation phase stopped growing. Galls treated in the growth phase grew slightly, primary nutritive tissue was replaced by a thick layer of proliferating callus, and lignified tissue appeared in its normal location. Galls treated in the maturation phase retained the arrangement of their secondary nutritive tissue but it degraded and callus did not develop in the larval chambers. We concluded that active larvae were necessary for normal gall growth and for the retention of primary nutritive cells, but larvae were not necessary for the formation of lignified tissues or for the retention of secondary nutritive cells.

Role of urophora cardui (l.) (diptera, tephritidae) in growth and development of its gall on stems of canada thistle

Cryoanalytical scanning electron microscopy was used to examine cellular concentrations of K, P, S, Mg, Ca, Fe, Cu, Ni, and Au in a planed section of an insect gall induced by Hemadas nubilipennis on shoots of lowbush blueberry. Levels of K varied throughout tissues of the gall, with the highest levels within the cytoplasmically dense nutritive cells lining the larval chambers, storage nutritive cells, and peridermal cells. It is postulated that K increases the osmotic potential and size of nutritive cells, thereby facilitating larval feeding. Nutritive cells also contained elevated levels of P and S. Levels of Cu, Ni, Fe, and Au were elevated in epidermal tissues, especially near the stomata. Key words: gall, blueberry, minerals, cryoanalytical SEM, Hemadas nubilipennis, Vaccinium angustifolium.

Mineral concentrations within cells of galls induced by Hemadas nubilipennis(Hymenoptera: Pteromalidae) on lowbush blueberry: evidence from cryoanalytical scanning electron microscopy.

The Biological Survey of Canada initiated a project in 1979 to collect and synthesise information on the native arthropod fauna of the vanishing grassland habitats of Canada. At that time, it was thought that the Canadian arthropod fauna might comprise about 66 000 species. Recent studies suggest that the fauna may exceed 100 000 species, of which >25% may occur in the Prairies Ecozone. Results of this near 40-year project have been published in four volumes of the Arthropods of Canadian Grasslands monograph series of the Biological Survey of Canada. Here, the editors of this series review the grasslands project of the Biological Survey of Canada, summarise the contents of the volumes, and discuss current knowledge on the diversity of the grasslands arthropods of Canada. Whereas information on the species richness of some groups in the Prairies Ecozone is largely complete, information on the diversity of many other groups remains sparse. Reviewing the steps between initiation and publication of the Arthropods of Canadian Grasslands series may aid development of similar projects elsewhere. Identifying knowledge gaps will direct future research efforts. Identifying the diversity of grassland arthropods, their distribution and abundance, and the ecosystem services that they provide will facilitate efforts to conserve the remaining grassland habitats in Canada.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/5E8C21BC0FA8D5A1F58114480D2966FB/S0008347X17000463a.pdf/div-class-title-arthropods-of-canadian-grasslands-a-retrospective-of-a-40-year-project-of-the-biological-survey-of-canada-div.pdf

Arthropods of Canadian grasslands: a retrospective of a 40-year project of the Biological Survey of Canada

The anthomyiid fly Pegomya curticornis (Stein), introduced into Alberta from Europe for the biocontrol of leafy spurge ( Euphorbia esula L.), normally induces simple galls on subterranean stems. Here we describe the anatomy of galls collected in Europe that had been induced by P . curticornis on horizontal roots of spurges. Four mature galls were found on the roots of E . virgata Waldst. and Kit. and 10 on the roots of E . esula . Tissues of the root galls were composed of gall parenchyma that had proliferated from feeding sites near the outside edge of secondary xylem. It is assumed that some larvae inadvertently tunnel beyond the base of stems into the roots and that similar galls will form on Alberta spurges.

Gall induction by Pegomya curticornis (Stein) (Diptera: Anthomyiidae) within the roots of spurges Euphorbia virgata Walkdst. and Kit. E. esula L. (Euphorbiaceae)

Joseph D. Shorthouse

Papers

Variability in the parasitoid community associated with galls of Diplolepis variabilis (Hymenoptera: Cynipidae): a test of the distance decay hypothesis

Role of urophora cardui (l.) (diptera, tephritidae) in growth and development of its gall on stems of canada thistle

Mineral concentrations within cells of galls induced by Hemadas nubilipennis(Hymenoptera: Pteromalidae) on lowbush blueberry: evidence from cryoanalytical scanning electron microscopy.

Arthropods of Canadian grasslands: a retrospective of a 40-year project of the Biological Survey of Canada

Gall induction by Pegomya curticornis (Stein) (Diptera: Anthomyiidae) within the roots of spurges Euphorbia virgata Walkdst. and Kit. E. esula L. (Euphorbiaceae)