We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

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The genome of the domesticated apple ( Malus × domestica Borkh.)

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

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The high-quality draft genome of peach ( Prunus persica ) identifies unique patterns of genetic diversity, domestication and genome evolution

Systemic insecticides are applied to plants using a wide variety of methods, ranging from foliar sprays to seed treatments and soil drenches. Neonicotinoids and fipronil are among the most widely used pesticides in the world. Their popularity is largely due to their high toxicity to invertebrates, the ease and flexibility with which they can be applied, their long persistence, and their systemic nature, which ensures that they spread to all parts of the target crop. However, these properties also increase the probability of environmental contamination and exposure of nontarget organisms. Environmental contamination occurs via a number of routes including dust generated during drilling of dressed seeds, contamination and accumulation in arable soils and soil water, runoff into waterways, and uptake of pesticides by nontarget plants via their roots or dust deposition on leaves. Persistence in soils, waterways, and nontarget plants is variable but can be prolonged; for example, the half-lives of neonicotinoids in soils can exceed 1,000 days, so they can accumulate when used repeatedly. Similarly, they can persist in woody plants for periods exceeding 1 year. Breakdown results in toxic metabolites, though concentrations of these in the environment are rarely measured. Overall, there is strong evidence that soils, waterways, and plants in agricultural environments and neighboring areas are contaminated with variable levels of neonicotinoids or fipronil mixtures and their metabolites (soil, parts per billion (ppb)-parts per million (ppm) range; water, parts per trillion (ppt)-ppb range; and plants, ppb-ppm range). This provides multiple routes for chronic (and acute in some cases) exposure of nontarget animals. For example, pollinators are exposed through direct contact with dust during drilling; consumption of pollen, nectar, or guttation drops from seed-treated crops, water, and consumption of contaminated pollen and nectar from wild flowers and trees growing near-treated crops. Studies of food stores in honeybee colonies from across the globe demonstrate that colonies are routinely and chronically exposed to neonicotinoids, fipronil, and their metabolites (generally in the 1–100 ppb range), mixed with other pesticides some of which are known to act synergistically with neonicotinoids. Other nontarget organisms, particularly those inhabiting soils, aquatic habitats, or herbivorous insects feeding on noncrop plants in farmland, will also inevitably receive exposure, although data are generally lacking for these groups. We summarize the current state of knowledge regarding the environmental fate of these compounds by outlining what is known about the chemical properties of these compounds, and placing these properties in the context of modern agricultural practices.

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Environmental fate and exposure; neonicotinoids and fipronil

Recent advances on the regulation of anthocyanin synthesis in reproductive organs

Aquaporins are membrane channels that facilitate the transport of water and small neutral molecules across biological membranes of most living organisms. In plants, aquaporins occur as multiple isoforms reflecting a high diversity of cellular localizations, transport selectivity, and regulation properties. Plant aquaporins are localized in the plasma membrane, endoplasmic reticulum, vacuoles, plastids and, in some species, in membrane compartments interacting with symbiotic organisms. Plant aquaporins can transport various physiological substrates in addition to water. Of particular relevance for plants is the transport of dissolved gases such as carbon dioxide and ammonia or metalloids such as boron and silicon. Structure-function studies are developed to address the molecular and cellular mechanisms of plant aquaporin gating and subcellular trafficking. Phosphorylation plays a central role in these two processes. These mechanisms allow aquaporin regulation in response to signaling intermediates such as cytosolic pH and calcium, and reactive oxygen species. Combined genetic and physiological approaches are now integrating this knowledge, showing that aquaporins play key roles in hydraulic regulation in roots and leaves, during drought but also in response to stimuli as diverse as flooding, nutrient availability, temperature, or light. A general hydraulic control of plant tissue expansion by aquaporins is emerging, and their role in key developmental processes (seed germination, emergence of lateral roots) has been established. Plants with genetically altered aquaporin functions are now tested for their ability to improve plant tolerance to stresses. In conclusion, research on aquaporins delineates ever expanding fields in plant integrative biology thereby establishing their crucial role in plants.

Aquaporins in Plants.

The family of aquaporins, also called water channels or major intrinsic proteins, is characterized by six transmembrane domains that together facilitate the transport of water and a variety of low molecular weight solutes. They are found in all domains of life, but show their highest diversity in plants. Numerous studies identified aquaporins as important targets for improving plant performance under drought stress. The phylogeny of aquaporins is well established based on model species like Arabidopsis thaliana, which can be used as a template to investigate aquaporins in other species. In this study we comprehensively identified aquaporin encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and also serves as a model for fleshy fruit development. We found 47 aquaporin genes in the tomato genome and analyzed their structural features. Based on a phylogenetic analysis of the deduced amino acid sequences the aquaporin genes were assigned to five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs) and their substrate specificity was assessed on the basis of key amino acid residues. As ESTs were available for 32 genes, expression of these genes was analyzed in 13 different tissues and developmental stages of tomato. We detected tissue-specific and development-specific expression of tomato aquaporin genes, which is a first step towards revealing the contribution of aquaporins to water and solute transport in leaves and during fruit development.

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Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

Aquaporins facilitate water transport across biomembranes in a manner dependent on osmotic pressure and water-potential gradient. The discovery of aquaporins has facilitated research on intracellular and whole-plant water transport at the molecular level. Aquaporins belong to a ubiquitous family of membrane intrinsic proteins (MIP). Plants have four subfamilies: plasma-membrane intrinsic protein (PIP), tonoplast intrinsic protein (TIP), nodulin 26-like intrinsic protein (NIP), and small basic intrinsic protein (SIP). Recent research has revealed a diversity of plant aquaporins, especially their physiological functions and intracellular localisation. A few PIP members have been reported to be involved in carbon dioxide permeability of cells. Newly identified transport substrates for NIP members of rice and Arabidopsis thaliana have been demonstrated to transport silicon and boron, respectively. Ammonia, glycerol, and hydrogen peroxide have been identified as substrates for plant aquaporins. The intracellular localisation of plant aquaporins is diverse; for example, SIP members are localised on the ER membrane. There has been much progress in the research on the functional regulation of water channel activity of PIP members including phosphorylation, formation of hetero-oligomer, and protonation of histidine residues under acidic condition. This review provides a broad overview of the range of potential aquaporins, which are now believed to participate in the transport of several small molecules in various membrane systems in model plants, crops, flowers and fruits.

Expanding roles of plant aquaporins in plasma membranes and cell organelles

The mobility of sugars between source and sink tissues in plants depends on sugar transport proteins. Studying the corresponding genes allows the manipulation of the sink strength of developing fruits, thereby improving fruit quality for human consumption. Tomato (Solanum lycopersicum) is both a major horticultural crop and a model for the development of fleshy fruits. In this article we provide a comprehensive inventory of tomato sugar transporters, including the SUCROSE TRANSPORTER family, the SUGAR TRANSPORTER PROTEIN family, the SUGAR FACILITATOR PROTEIN family, the POLYOL/MONOSACCHARIDE TRANSPORTER family, the INOSITOL TRANSPORTER family, the PLASTIDIC GLUCOSE TRANSLOCATOR family, the TONOPLAST MONOSACCHARIDE TRANSPORTER family and the VACUOLAR GLUCOSE TRANSPORTER family. Expressed sequence tag (EST) sequencing and phylogenetic analyses established a nomenclature for all analyzed tomato sugar transporters. In total we identified 52 genes in tomato putatively encoding sugar transporters. The expression of 29 sugar transporter genes in vegetative tissues and during fruit development was analyzed. Several sugar transporter genes were expressed in a tissue- or developmental stage-specific manner. This information will be helpful to better understand source to sink movement of photoassimilates in tomato. Identification of fruit-specific sugar transporters might be a first step to find novel genes contributing to tomato fruit sugar accumulation.

The sugar transporter inventory of tomato: genome-wide identification and expression analysis.

The vacuole is by far the largest organelle in fruits and can occupy more than 90 percent of the cell volume. Therefore, if we eat fruits and their products, we mainly eat the compounds stored within the vacuole. The main compounds are sugars, organic acids and secondary metabolites, such as phenolics and terpenoids, that are important for fruit quality. High concentrations of sugars, organic acids and inorganic ions in fruits generate a high osmotic pressure leading to a strong negative water potential that attracts water, allowing the fruit to grow. Accumulation of solutes within the vacuole requires many transporters in the vacuolar membrane, which is also called tonoplast. This review summarizes studies of transporters in fruit vacuoles, including proton pumps, aquaporins, sugar transporters, organic acid transporters and ABC transporters.

https://www.jstage.jst.go.jp/article/plantbiotechnology/24/1/24_1_127/_pdf

Transporters in fruit vacuoles

;Sorbitol is a major photosynthetic product and a major phloem-translocated component in Rosaceae (e.g. apple, pear, peach, and cherry). We isolated the three cDNAs, MdSOT3, MdSOT4, and MdSOT5 from apple (Malus domestica) source leaves, which are homologous to plant polyol transporters. Yeasts transformed with the MdSOTs took up sorbitol significantly. MdSOT3- and MdSOT5-dependent sorbitol uptake was strongly inhibited by xylitol and myo-inositol, but not or only weakly by mannitol and dulcitol. Apparent Km values of MdSOT3 and MdSOT5 for sorbitol were estimated to be 0.71 mM and 3.2 mM, respectively. The protonophore, carbonyl cyanide m-chlorophenylhydrazone (CCCP), strongly inhibited the sorbitol transport. MdSOT3 was expressed specifically in source leaves, whereas MdSOT4 and MdSOT5 were expressed in source leaves and also in some sink organs. MdSOT4 and MdSOT5 expressions were highest in flowers. Fruits showed no or only weak MdSOT expression. Although MdSOT4 and MdSOT5 were also expressed in immature leaves, MdSOT expressions increased with leaf maturation. In addition, in situ hybridization revealed that all MdSOTs were expressed to high levels in phloem of minor veins in source leaves. These results suggest that these MdSOTs are involved in sorbitol loading in Rosaceae.

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Katsuhiro Shiratake

Papers

Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

Expanding roles of plant aquaporins in plasma membranes and cell organelles

The sugar transporter inventory of tomato: genome-wide identification and expression analysis.

Transporters in fruit vacuoles

Identification of Sorbitol Transporters Expressed in the Phloem of Apple Source Leaves