Data-processing in phytosociology,retrospect and anticipation

Summary The existence of the Working Group for Data-Processing in Phytosociology spans about six years, 1969–1975. Its activities are summarized and a series of papers to appear in Vegetatio, presenting results of various numerical treatments, mainly of salt marsh vegetation, is introduced. A survey is given of seven releve selections to which treatments were applied. Five main fields of activities are discussed: systematical data-processing, rearrangement of phytosociological tables, development of classification and ordination techniques, numerical syntaxonomy, and theoretical phytosociology.The establishment of the Working Group for Theoretical Phytosociology and its first symposium on theoretical aspects is announced.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science.     

Game theory and plant ecology

The fixed and plastic traits possessed by a plant, which may be collectively thought of as its strategy, are commonly modelled as density‐independent adaptations to its environment. However, plant strategies may also represent density‐ or frequency‐dependent adaptations to the strategies used by neighbours. Game theory provides the tools to characterise such density‐ and frequency‐dependent interactions. Here, we review the contributions of game theory to plant ecology. After briefly reviewing game theory from the perspective of plant ecology, we divide our review into three sections. First, game theoretical models of allocation to shoots and roots often predict investment in those organs beyond what would be optimal in the absence of competition. Second, game theoretical models of enemy defence suggest that an individual's investment in defence is not only a means of reducing its own tissue damage but also a means of deflecting enemies onto competitors. Finally, game theoretical models of trade with mutualistic partners suggest that the optimal trade may reflect competition for access to mutualistic partners among plants. In short, our review provides an accessible entrance to game theory that will help plant ecologists enrich their research with its worldview and existing predictions.     

Subunit‐selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections

The proteasome is a nuclear‐cytoplasmic proteolytic complex involved in nearly all regulatory pathways in plant cells. The three different catalytic activities of the proteasome can have different functions, but tools to monitor and control these subunits selectively are not yet available in plant science. Here, we introduce subunit‐selective inhibitors and dual‐color fluorescent activity‐based probes for studying two of the three active catalytic subunits of the plant proteasome. We validate these tools in two model plants and use this to study the proteasome during plant–microbe interactions. Our data reveal that Nicotiana benthamiana incorporates two different paralogs of each catalytic subunit into active proteasomes. Interestingly, both β1 and β5 activities are significantly increased upon infection with pathogenic Pseudomonas syringae pv. tomato DC3000 lacking hopQ1‐1 [PtoDC3000(ΔhQ)] whilst the activity profile of the β1 subunit changes. Infection with wild‐type PtoDC3000 causes proteasome activities that range from strongly induced β1 and β5 activities to strongly suppressed β5 activities, revealing that β1 and β5 activities can be uncoupled during bacterial infection. These selective probes and inhibitors are now available to the plant science community, and can be widely and easily applied to study the activity and role of the different catalytic subunits of the proteasome in different plant species.     

Strong between‐site variation in New Caledonian crows’ use of hook‐tool‐making materials

Functional tool use requires the selection of appropriate raw materials. New Caledonian crows Corvus moneduloides are known for their extraordinary tool‐making behaviour, including the crafting of hooked stick tools from branched vegetation. We describe a surprisingly strong between‐site difference in the plant materials used by wild crows to manufacture these tools: crows at one study site use branches of the non‐native shrub Desmanthus virgatus, whereas only approximately 7 km away, birds apparently ignore this material in favour of the terminal twigs of an as‐yet‐unidentified tree species. Although it is likely that differences in local plant communities drive this striking pattern, it remains to be determined how and why crows develop such strong site‐specific preferences for certain raw materials.     

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.     

Strategies for complete plastid genome sequencing

Plastid sequencing is an essential tool in the study of plant evolution. This high‐copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low‐cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation‐sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short‐range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.     

Ranking species based on the components of equivocation information

Summary The results presented in this paper suggest that for species to be weighted according to their suitability to characterize isolated groups of relevés in a phytosociological table, the equivocation information may serve as a suitable weight. The appropriate formulations are derived and computed for some data from a salt marsh community.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science.The author thanks the National Research Council of Canada for support given.     

Six new polymorphic microsatellite loci isolated and characterized from the African savannah elephant genome

The African savannah elephant (Loxodonta africana) is a ‘keystone’ species that plays a vital role in regulating the dynamics of both plant and animal communities and yet it is endangered and its numbers have been reduced to approximately 500 000 across their entire continental range. Molecular genetic markers are important tools for providing genetic information useful in formulating effective management and conservation strategies for the surviving elephant populations. We describe the isolation and characterization of six new polymorphic microsatellite markers in the African savannah elephant and demonstrate that these loci can be PCR (polymerase chain reaction)‐multiplexed, a desirable attribute that saves costs in large‐scale microsatellite screening.     

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant–microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant‐associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant–microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil‐borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere‐related traits, (c) the role of root exudation in microbe‐mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.     

Tissue‐specific inactivation by cytosine deaminase/uracil phosphoribosyl transferase as a tool to study plant biology

Recent advances in the study of plant developmental and physiological responses have benefited from tissue‐specific approaches, revealing the role of some cell types in these processes. Such approaches have relied on the inactivation of target cells using either toxic compounds or deleterious genes; however, both tissue‐specific and truly inducible tools are lacking in order to precisely target a developmental window or specific growth response. We engineered the yeast fluorocytosine deaminase (FCY1) gene by creating a fusion with the bacterial uracil phosphoribosyl transferase (UPP) gene. The recombinant protein converts the precursor 5‐fluorocytosine (5‐FC) into 5‐fluorouracyl, a drug used in the treatment of a range of cancers, which triggers DNA and RNA damage. We expressed the FCY‐UPP gene construct in specific cell types using enhancer trap lines and promoters, demonstrating that this marker acts in a cell‐autonomous manner. We also showed that it can inactivate slow developmental processes like lateral root formation by targeting pericycle cells. It also revealed a role for the lateral root cap and the epidermis in controlling root growth, a faster response. The 5‐FC precursor acts systemically, as demonstrated by its ability to inhibit stomatal movements when supplied to the roots in combination with a guard cell‐specific promoter. Finally, we demonstrate that the tissular inactivation is reversible, and can therefore be used to synchronize plant responses or to determine cell type‐specific functions during different developmental stages. This tool will greatly enhance our capacity to understand the respective role of each cell type in plant physiology and development.     

Effectiveness of modern leaf analysis tools for the morpho‐ecological study of plants: the case of Primula albenensis

Scientific and technological progress has led to the creation of analysis tools that have revolutionized traditional studies in morphology and plant ecology. Recently developed methods and tools which, on the basis of leaf samples, allow for geometric morphometric analyses and the evaluation of functional strategies are good examples. These methods, still little used, have never been applied on leaf samples to simultaneously obtain information on their morphometry and the ecology of the plants. This article discusses the effectiveness of modern leaf analysis tools for geometric morphometrics (outline analysis) and studies of functional strategies based on the competitor‐stress tolerator‐ruderal (CSR) scheme, using a study of a steno‐endemic plant of the Alps, Primula albenensis Banfi et Ferl. as an example. These aspects were analyzed using leaf samples collected in the only two areas where this species grows. CSR analyses revealed that P. albenensis is not a stress‐tolerant species (C:S:R = 37:1:62), as previously thought. Moreover, no significant intraspecific differences in functional strategy were revealed. Instead, outline analysis highlighted a significant difference (p < 0.001) between leaves collected from the two sampling areas. The results of this study and others reported in the literature therefore suggest that these modern methods of leaf analysis are cheap, effective and relatively simple to perform. Furthermore, researchers are able to carry out geometric morphometric and CSR analysis using the same samples of leaves in order to maximize the information content provided by the analysis of a plant material which may not be easily available.     

High‐throughput two‐dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

High‐throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user‐guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large‐scale phenotyping studies. To demonstrate the unique capabilities and high‐throughput capacity of this phenotyping platform for studying root systems, genome‐wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population.     

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome‐wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass‐spectrometry‐based analytical systems and genome sequencing technologies. Metabolic genome‐wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS‐based multi‐dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS‐based multi‐dimensional analysis and emerging insights into the diversity of metabolism.     

Introduced Lantana camara used as tools by New Caledonian crows (Corvus moneduloides)

Abstract

New Caledonian crows commonly use sticks and similar plant material as hooked and non‐hooked tools to extract prey. They are known to target certain tree species that produce twigs of the right natural shape for easy conversion into tools. All previously identified species supplying tool materials have been native or endemic to New Caledonia. Here I report that crows living in disturbed habitats also use the barbed twigs of an introduced climbing plant, Lantana camara, as tools. Over an 8‐year period I collected 12 L. camara tools used by NC crows at three locations: Bourail and Sarraméa, on mainland Grande Terre, and on the island of Maré. I found these tools left in natural probe sites (Bourail and Sarraméa) or at artificial feeding sites (Maré), but I do not know if the crows targeted L. camara or simply used the closest suitable material. Nevertheless, the use of L. camara indicates that the behaviour of certain free‐living NC crows is sufficiently flexible to enable them to evaluate and use exotic plants for tool material.     

Recent insights into cotton functional genomics: progress and future perspectives

Functional genomics has transformed from futuristic concept to well‐established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re‐sequencing broad diversity panels with the development of high‐throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.     

High‐throughput physiological phenotyping and screening system for the characterization of plant–environment interactions

We present a simple and effective high‐throughput experimental platform for simultaneous and continuous monitoring of water relations in the soil–plant–atmosphere continuum of numerous plants under dynamic environmental conditions. This system provides a simultaneously measured, detailed physiological response profile for each plant in the array, over time periods ranging from a few minutes to the entire growing season, under normal, stress and recovery conditions and at any phenological stage. Three probes for each pot in the array and a specially designed algorithm enable detailed water‐relations characterization of whole‐plant transpiration, biomass gain, stomatal conductance and root flux. They also enable quantitative calculation of the whole plant water‐use efficiency and relative water content at high resolution under dynamic soil and atmospheric conditions. The system has no moving parts and can fit into many growing environments. A screening of 65 introgression lines of a wild tomato species (Solanum pennellii) crossed with cultivated tomato (S. lycopersicum), using our system and conventional gas‐exchange tools, confirmed the accuracy of the system as well as its diagnostic capabilities. The use of this high‐throughput diagnostic screening method is discussed in light of the gaps in our understanding of the genetic regulation of whole‐plant performance, particularly under abiotic stress.     

Plant Peroxisome Multiplication： Highly Regulatec and Still Enigmatic

Plant peroxisomes play a key role in numerous physiological processes and are able to adapt to environmental changes by altering their content, morphology, and abundance. Peroxisomes can multiply through elongation, constriction, and fission; this process requires the action of conserved, as well as species-specific proteins. Genetic and morphological analyses have been used with the model plant Arabidopsis thaliana to determine at the mechanistic level how plant peroxisomes increase their abundance. The five-member PEXll family promotes early steps of peroxisome multiplication with an unknown mechanism and some subfamily specificities. The dynamin-related protein （DRP）3 subfamily of dynaminrelated large guanosine triphosphatases mediates late steps of both peroxisomal and mitochondrial multiplication. New genetic and biochemical tools will be needed to identify additional, especially plant-specific, constituents of the peroxisome multiplication pathways.     

Phylogenetic analysis reveals positive correlations between adaptations to diverse hosts in a group of pathogen‐like herbivores

A jack of all trades can be master of none—this intuitive idea underlies most theoretical models of host‐use evolution in plant‐feeding insects, yet empirical support for trade‐offs in performance on distinct host plants is weak. Trade‐offs may influence the long‐term evolution of host use while being difficult to detect in extant populations, but host‐use evolution may also be driven by adaptations for generalism. Here we used host‐use data from insect collection records to parameterize a phylogenetic model of host‐use evolution in armored scale insects, a large family of plant‐feeding insects with a simple, pathogen‐like life history. We found that a model incorporating positive correlations between evolutionary changes in host performance best fit the observed patterns of diaspidid presence and absence on nearly all focal host taxa, suggesting that adaptations to particular hosts also enhance performance on other hosts. In contrast to the widely invoked trade‐off model, we advocate a “toolbox” model of host‐use evolution in which armored scale insects accumulate a set of independent genetic tools, each of which is under selection for a single function but may be useful on multiple hosts.     

Arabidopsis phosphatidylinositol 4‐phosphate 5‐kinase 2 contains a functional nuclear localization sequence and interacts with alpha‐importins

The Arabidopsis phosphoinositide kinase PIP5K2 has been implicated in the control of membrane trafficking and is important for development and growth. In addition to cytosolic functions of phosphoinositides, a nuclear phosphoinositide system has been proposed, but evidence for nuclear phosphoinositides in plants is limited. Fluorescence‐tagged variants of PIP5K2 reside in the nucleus of Arabidopsis root meristem cells, in addition to reported plasma membrane localization. Here we report on the interaction of PIP5K2 with alpha‐importins and characterize its nuclear localization sequences (NLSs). The PIP5K2 sequence contains four putative NLSs (NLSa–NLSd) and only a PIP5K2 fragment containing NLSs is imported into nuclei of onion epidermis cells upon transient expression. PIP5K2 interacts physically with alpha‐importin isoforms in cytosolic split‐ubiquitin‐based yeast two‐hybrid tests, in dot‐blot experiments and in immuno‐pull‐downs. A 27‐amino‐acid fragment of PIP5K2 containing NLSc is necessary and sufficient to mediate the nuclear import of a large cargo fusion consisting of two mCherry markers fused to RubisCO large subunit. Substitution of basic residues in NLSc results in reduced import of PIP5K2 or other cargoes into plant nuclei. The data suggest that PIP5K2 is subject to active, alpha‐importin‐mediated nuclear import, consistent with a nuclear role for PIP5K2 in addition to its reported cytosolic functions. The detection of both substrate and product of PIP5K2 in plant nuclei according to reporter fluorescence and immunofluorescence further supports the notion of a nuclear phosphoinositide system in plants. Variants of PIP5K2 with reduced nuclear residence might serve as tools for the future functional study of plant nuclear phosphoinositides.