LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology

Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.

Niche and neutral processes leave distinct structural imprints on indirect interactions in mutualistic networks

Indirect interactions are central to ecological and evolutionary dynamics in pollination communities, yet we have little understanding about the processes determining patterns of indirect interactions, such as those between pollinators through shared flowering plants. Instead, research has concentrated on the processes responsible for direct interactions and whole-network structures. This is partly due to a lack of appropriate tools for characterising indirect interaction structures, because traditional network metrics discard much of this information. The recent development of tools for counting motifs (subnetworks depicting interactions between a small number of species) in bipartite networks enable detailed analysis of indirect interaction patterns. Here we generate plant-hummingbird pollination networks based on three major assembly processes – neutral effects (species interacting in proportion to abundance), morphological matching and phenological overlap – and evaluate the motifs associated with each one. We find that different processes produce networks with significantly different patterns of indirect interactions. Neutral effects tend to produce densely-connected motifs, with short indirect interaction chains, and motifs where many specialists interact indirectly through a single generalist. Conversely, niche-based processes (morphology and phenology) produced motifs with a core of interacting generalists, supported by peripheral specialists. These results have important implications for understanding the processes determining indirect interaction structures.

Research in Forest Biology in the Era of Climate Change and Rapid Urbanization

Green plants provide the foundation for the structure, function, and interactions among organisms in both tropical and temperate zones. To date, many investigations have revealed patterns and mechanisms that generate plant diversity at various scales and from diverse ecological perspectives. However, in the era of climate change, anthropogenic disturbance, and rapid urbanization, new insights are needed to understand how plant species in these forest habitats are changing and adapting. Here, we recognize four themes that link studies from Asia and Europe presented in this Special Issue: (1) genetic analyses of diverse plant species; (2) above- and below-ground forest biodiversity; (3) trait expression and biological mechanisms; and (4) interactions of woody plants within a changing environment. These investigations enlarge our understanding of the origins of diversity, trait variation and heritability, and plant–environment interactions from diverse perspectives.

NOMENCLATURAL TYPES OF THE TAXA NAMED AFTER N. I. VAVILOV IN THE HERBARIUM COLLECTION OF VIR (WIR)

Carl Linnaeus believed, even in his time, that na-mes of eminent scientists may serve as a good source to generate plant names. In 2017, the 130th birthday anniversary of Nikolai Ivanovich Vavilov, an outstanding biologist of the twentieth century, was celebrated. The magnitude of his personality and his tremendous contribution to the knowledge of the world’s diversity of cultivated plants and their wild relatives compelled many taxonomists to use Vavilov’s name while naming new plant taxa. All in all, 28 botanical taxa with Vavilov’s name have been made public: one genus and 27 species, including intraspecific taxa. One third of them are taxa within the genus Triticum L. (one species, one subspecies, and seven varieties). Nomenclatural types of seven taxa are preserved in VIR’s herbarium (WIR). These are represented by holotypes and mesotypes: Aegilops crassa subsp. vavilovii Zhuk. (≡ A. vavilovii (Zhuk.) Chennav.) and Triticum spelta subsp. kuckuckianum var. vavilovii Dorof.; lectotypes and isolectotypes: Avena strigosa subsp. vaviloviana Malz. (≡ A. vaviloviana (Malz.) Mordv.) and Solanum vavilovii Juz. et Buk.; and neotypes: Triticum aestivum var. vavilovianum Jakubz., T. dicoccoides var. vavilovii Jakubz., and T. vulgare var. vavilovii Thum. (≡ T. vavilovii (Thum.) Jakubz.).

Engineered Root Bacteria Release Plant-Available Phosphate from Phytate

ABSTRACTMicroorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging phosphate fertilizers. To explore this possibility, we engineered a collection of root bacteria to release plant-available orthophosphate from phytate, an abundant phosphate source in many soils. We identified 82 phylogenetically diverse phytase genes, refactored their sequences for optimal expression inProteobacteria, and then synthesized and engineered them into the genomes of three root-colonizing bacteria. Liquid culture assays revealed 41 engineered strains with high levels of phytate hydrolysis. Among these, we identified 12 strains across three bacterial hosts that confer a growth advantage on the model plantArabidopsis thalianawhen phytate is the sole phosphate source. These data demonstrate that DNA synthesis approaches can be used to generate plant-associated strains with novel phosphate-solubilizing capabilities.IMPORTANCEPhosphate fertilizers are essential for high-yield agriculture yet are costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil are appealing, as they may reduce the need for such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with the ability to release phosphate from phytate. We demonstrate that these strains improve plant growth under phosphorus-limited conditions. This represents a first step in the development of phosphate-mining bacteria for future use in crop systems.

Computational design of environmental sensors for the potent opioid fentanyl

We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.

Welcome to Phytobiomes

In 2014, members of The American Phytopathological Society (APS) began to consider strategically the ways in which the accelerating flow of diverse types of complex data are fundamentally changing the ways in which we study, think about, and manage plant systems. Advancing technical capacities to generate plant, microbial and other organismal ‘omics’, environmental, and data produced at very fine spatial scales, coupled with expanding capabilities to integrate data across diverse scales of space and time, are providing novel insights into the networks of interaction that mediate plant productivity. In response to these enormous advances in technical capacities, APS created a Phytobiomes Initiative to chart a path forward. In 2015, APS brought together a diverse community of scientists in Washington DC for a strategically timed meeting to spearhead a new paradigm for crop improvement focusing on phytobiome-based approaches. The success of the human microbiome project paved the way, challenging us to push the boundaries to expand our knowledge of sustainable agriculture to meet the demands of feeding the growing global population. This meeting was instrumental in clarifying the vision of phytobiomes research, encapsulating systems-level understanding of diverse interacting components spanning multiple disciplines, species, and environments. To fully appreciate the breadth of scope of the Phytobiomes Initiative, we encourage you to review the Phytobiomes Roadmap ( http://www.phytobiomes.org/roadmap ), released in March 2016. The Phytobiomes journal was launched as an integral but independent part of the Phytobiomes Initiative. The Phytobiomes journal provides an international platform for fundamental, translational, and integrated research that accomplishes the overarching objective of offering a new vision for agriculture in which sustainable crop productivity is achieved through a systems-level understanding of the diverse interacting components of the phytobiome. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY Attribution 4.0 International license .

Induced defenses alter the strength and direction of natural selection on reproductive traits in common milkweed

Evolutionary biologists have long sought to understand the ecological processes that generate plant reproductive diversity. Recent evidence indicates that constitutive antiherbivore defenses can alter natural selection on reproductive traits, but it is unclear whether induced defenses will have the same effect and whether reduced foliar damage in defended plants is the cause of this pattern. In a factorial field experiment using common milkweed, Asclepias syriaca, we induced plant defenses using jasmonic acid (JA) and imposed foliar damage using scissors. We found that JA-induced plants experienced selection for more inflorescences that were smaller in size (fewer flowers), while control plants only experienced a trend toward selection for larger inflorescences (more flowers); all effects were independent of foliar damage. Our results demonstrate that induced defenses can alter both the strength and direction of selection on reproductive traits, and suggest that antiherbivore defenses may promote the evolution of plant reproductive diversity.