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

Sections of stem galls induced by Diplolepis triforma Shorthouse and Ritchie obtained by plant histological techniques were used to examine anatomical features of immature stages of the insect found in situ. First-instar larvae feed over the entire surface of larval chambers, whereas maturing larvae feed only at one end of the chambers. Last-instar larvae undergo two phases of development: feeding occurs in the first phase, whereas in the second, or prepupal phase, feeding has ceased, the mid- and hind-guts become joined, contents of the gut are voided, and compound eyes, gonads, and internal ovipositional apparatus begin to differentiate. The prepupal phase also consists of two phases: the first occurs in the fall and winter, and the second occurs in the spring prior to pupation. The spring phase exhibits external adult features within the integument of the last-instar and moults to the pupa. Sections of some maturing larvae contained endoparasitoid larvae of the genus Orthopelma Taschenberg (Hymenoptera: Ichneumonidae).

Immature stages of the galler Diplolepis triforma (Hymenoptera: Cynipidae) with comments on the role of its prepupa

The leaf galler Diplolepis polita (Ashmead), known only from Rosa acicularis Lindl. west of the Rocky Mountains, is recorded for the first time on the introduced, urban shrub rose Rosa rugosa Thunb. Inquilines and parasitoids commonly kill over 90% of the inducers in populations of galls found in natural habitats, whereas 55% of the galls from the urban roses contained an inducer. Differences in component communities associated with galls on domestic and wild roses are likely indicative of a recently established population in an atypical habitat. Occurrence of D. polita on this new host also provides insight into the host specificity and vagility of cynipid wasps.

Host shift of the leaf galler diplolepis polita (hymenoptera: cynipidae) to the domestic shrub rose rosa rugosa

The cynipid Diplolepis triforma Shorthouse and Ritchie induces a fusiform, multi chambered stem gall from leaf buds on Rosa acicularis Lindl. in central and western Canada. Galls at all stages of development were fixed and sectioned using botanical histological techniques to illustrate, for the first time, the unique host-modifying abilities of gall-inducing cynipids that distinguish them from other phytophagous insects. Key events in gall ontogeny, whereby D. triforma gains control and redirects the development of attacked host tissues to provide larvae with shelter and food, include proliferation of cytoplasmically dense parenchymatous cells within the strands of the procambium at the point of egg contact, appearance of nutritive cells when larvae first begin to feed, formation of new xylem and phloem extending from un affected vascular bundles to the larval chambers, formation of several layers of nutritive cells during the period of larval feeding, and formation of sclerenchyma cells around each larval chamber. The role of these tissues in galler biology is explained.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0008347X00004624

Development of stem galls induced by Diplolepis triforma (Hymenoptera: Cynipidae) on Rosa acicularis (Rosaceae)

The species of Synophromorpha Ashmead (Hymenoptera: Cynipidae) are reviewed. One new species is described (Synophromorpha kaulbarsi; type locality: Naupan, Puebla, Mexico). The previously described species (S. rubi Weld, S. sylvestris (O.S.), and S. terricola Weld) are redescribed, and a key to species is presented. All species are illustrated for the first time. Synophromorpha sylvestris is designated type-species for the genus and a lectotype is chosen. Hypotheses on the phylogenetic relationships between the species of Synophromorpha are presented.

Revision of the genus Synophromorpha Ashmead (Hymenoptera: Cynipidae)

Leafy spurge (Euphorbia × pseudovirgata [Schur]) is an herbaceous perennial and serious weed of European origin that has been accidently introduced into North America. The European anthomyiid flies Pegomya curticornis (Stein) and Pegomya euphorbiae (Kieffer) are found on several spurge species in Europe and also attack leafy spurge. The two flies induce identical galls on the subterranean stems of their host plants, and the shoots wilt and die. Eggs are laid on the shoot tip, and the larvae bore into the stem by eating pith which is later replaced by callus. This is a rare example of an insect with both boring and gall-inducing feeding strategies. Galls are induced when larvae feed on the ring of vascular tissue. There is no proliferation of nutritive cells but instead thick layers of gall parenchyma are produced. The vascular connections are broken at the gall level and concentric vascular bundles appear in the cortical and gall parenchyma. After pupation an inner periderm differentiates around the chamber surface.

Structural damage and gall induction by Pegomya curticornis and Pegomya euphorbiae (Diptera: Anthomyiidae) within the stems of leafy spurge (Euphorbia × pseudovirgata) (Euphorbiaceae).

Joseph D. Shorthouse

Papers

Immature stages of the galler Diplolepis triforma (Hymenoptera: Cynipidae) with comments on the role of its prepupa

Host shift of the leaf galler diplolepis polita (hymenoptera: cynipidae) to the domestic shrub rose rosa rugosa

Development of stem galls induced by Diplolepis triforma (Hymenoptera: Cynipidae) on Rosa acicularis (Rosaceae)

Revision of the genus Synophromorpha Ashmead (Hymenoptera: Cynipidae)

Structural damage and gall induction by Pegomya curticornis and Pegomya euphorbiae (Diptera: Anthomyiidae) within the stems of leafy spurge (Euphorbia × pseudovirgata) (Euphorbiaceae).