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

Gall-inducing insects – Nature's most sophisticated herbivores

Gall inducers are favoured as biocontrol agents of weeds because they tend to have a narrow host range. Six insect and one nematode gall inducer used in Canada are described in terms of their biology, gall morphology, gall physiology, and effectiveness in weed control. The species differ in plant organ attacked, requirement for moisture, whether the galls are induced by secretions or by severing xylem, and effectiveness, which in part relates to the ability of the gall to import nutrients. The most powerful galls divert assimilates from other sinks via a gall’s vascular system joined to that of their host. One of our examples also has mechanisms to compensate for reduction of turgor during drought. Two of the gall inducers enhance their nutrient supply by severing xylem in a plant nutrient sink. One, in the short-term sink of a thistle capitulum, obtains about a quarter of its assimilates at the expense of other capitula. The other, in the long-term sink of a rosette root, approximately halves seed production. Hypotheses are presented to explain various aspects of gall development and function.

Effectiveness of gall inducers in weed biological control

Prepupae of the rose galling Diplolepis spinosa from areas with relatively cold winters in southern Canada, and Diplolepis variabilis from a milder locale in western Canada, were used to test the hypothesis that mild winter temperatures are detrimental to the survival and potential fecundity of insects. Prepupae of D. spinosa held within or removed from their galls were exposed to simulated overwintering temperatures (-22, 0, 5, or 10 degrees C) for approximately four months before measuring their survival, body size, and potential fecundity. Similar studies were conducted using prepupae of D. variabilis that were removed from their gall and subjected to 0 degrees C or 10 degrees C treatments. Diplolepis spinosa, with or without their galls, averaged 66% more mortality at 10 degrees C than at 0 degrees C. Female D. spinosa that survived the 10 degrees C treatment had 32% fewer eggs than those held at 0 degrees C. In contrast, there was no difference in survival or numbers of eggs between D. variabilis held at 0 degrees C and 10 degrees C. Body size of adult females and size of eggs did not differ among temperature treatments for either species. We conclude that mild overwintering temperatures may be detrimental for insects by raising their metabolism, and consequently reducing energetic reserves needed for development to the adult stage and subsequent production of eggs the following spring.

Deleterious effects of mild simulated overwintering temperatures on survival and potential fecundity of rose-galling Diplolepis wasps (Hymenoptera: Cynipidae).

Diplolepis nodulosa (Beutenmuller) induces small, single-chambered, prosoplasmic galls in stems of Rosa blanda Ait. Gall initiation begins when adult females deposit a single egg into the procambium of R. blanda buds. Pith cells at the distal pole of the egg lyse forming a chamber into which the hatching larva enters. Cells lining the chamber differentiate into nutritive cells, which serve as the larval food. Gall growth is characterized by the proliferation of parenchymatous nutritive cells causing gall enlargement. A separate gall vasculature does not form, but instead, gall tissues are irrigated by the existing stem vasculature. Maturation begins when gall tissues cease proliferating and differentiate into distinct layers concentrically arranged around the larval chamber. The innermost layer is composed of cytoplasmically dense nutritive tissue, followed by parenchymatous nutritive tissue, sclerenchyma, cortex, and epidermis. Parenchymatous nutritive tissue differentiates into nutritive tissue and is c...

Developmental morphology of stem galls of Diplolepis nodulosa (Hymenoptera: Cynipidae) and those modified by the inquiline Periclistus pirata (Hymenoptera: Cynipidae) on Rosa blanda (Rosaceae)

We report that a chemical stimulus from a herbivore, a galling insect, changes plant morphology and physiology to benefit the herbivore Previous studies could not determine whether insect galls are induced by mechanical or chemical stimuli because feeding and oviposition both occurred at the site of gall formation We report that the mouthparts of a spruce-galling insect, Adelges cooleyi, were inserted in stem phloem cells far from induced galls, that tissues between mouthparts and galls appeared normal, and that the ability to initiate galls was inversely correlated with distance from buds (potential gall sites) Thus the effects of chemical stimuli were unambiguously separated from any mechanical influence of probing stylets or ovipositors Our results strongly suggest that galls were induced by a chemical stimulus transported to buds via vascular tissue and that its efficacy was dose-dependent

Joseph D. Shorthouse

Papers

Gall-inducing insects – Nature's most sophisticated herbivores

Effectiveness of gall inducers in weed biological control

Deleterious effects of mild simulated overwintering temperatures on survival and potential fecundity of rose-galling Diplolepis wasps (Hymenoptera: Cynipidae).

Developmental morphology of stem galls of Diplolepis nodulosa (Hymenoptera: Cynipidae) and those modified by the inquiline Periclistus pirata (Hymenoptera: Cynipidae) on Rosa blanda (Rosaceae)

Evidence for long‐distance, chemical gall induction by an insect