The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 1943 coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these,~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C39H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

The immunophilin-like FKBP42 TWISTED DWARF1 (TWD1) has been shown to control plant development via the positive modulation of ABCB/P-glycoprotein (PGP)-mediated transport of the plant hormone auxin. TWD1 functionally interacts with two closely related proteins, ABCB1/PGP1 and ABCB19/PGP19/MDR1, both of which exhibit the ability to bind to and be inhibited by the synthetic auxin transport inhibitor N-1-naphylphtalamic acid (NPA). They are also inhibited by flavonoid compounds, which are suspected modulators of auxin transport. The mechanisms by which flavonoids and NPA interfere with auxin efflux components are unclear. We report here the specific disruption of PGP1-TWD1 interaction by NPA and flavonoids using bioluminescence resonance energy transfer with flavonoids functioning as a classical established inhibitor of mammalian and plant PGPs. Accordingly, TWD1 was shown to mediate modulation of PGP1 efflux activity by these auxin transport inhibitors. NPA bound to both PGP1 and TWD1 but was excluded from the PGP1-TWD1 complex expressed in yeast, suggesting a transient mode of action in planta. As a consequence, auxin fluxes and gravitropism in twd1 roots are less affected by NPA treatment, whereas TWD1 gain-of-function promotes root bending. Our data support a novel model for the mode of drug-mediated P-glycoprotein regulation mediated via protein-protein interaction with immunophilin-like TWD1.Bioactive flavonoids derived from plant secondary metabolism serve as important nutraceuticals (1). They have healthpromoting effects, including antioxidant, anticarcinogenic, antiviral, and anti-inflammatory activities; however, the cellular targets of the in vivo protein remain largely unknown (1, 2). In plants, among other functions, flavonoids such as quercetin, kaempferol, and other aglycone molecules have been shown to inhibit cell-to-cell/polar auxin transport (PAT) 3 and consequently to enhance localized auxin accumulation (1, 3-6). During PAT, the plant hormone auxin, which determines many aspects of plant physiology and development, is moved directionally in a cell-to-cell mode (7-9).The regulatory impact of flavonoids on PAT initially was based on their ability to compete with N-1-naphtylphtalamic acid (NPA), a synthetic auxin transport inhibitor (ATI) (4, 10 -12) and herbicide (naptalam, alanap), for transporter binding sites. This concept is further supported by auxin-related phenotypes of Arabidopsis mutants with altered flavonoid levels (1, 3, 13), although fundamental physiological processes occur in the absence of flavonoids. Currently the flavonoids are seen as transport regulators or modulators (14); nevertheless, the mechanisms by which flavonoids interfere with auxin efflux components are not yet clear (1).The auxin efflux complex is thought to regulate PAT on the molecular level and consists of at least two proteins: a membrane integral transporter and an NPA-binding protein (NBP) regulatory subunit (11,(15)(16)(17). Recently, ABCB/P-glycoprotein (PGP)/multidrug resistance (MDR) proteins, members o...

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Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1). We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstream locations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity.

With its long history of cultivation, the domesticated apple, Malus × domestica Borkh., is an excellent model for studying domestication in long-lived perennial plants. As apples have been transported from their center of origin in the Tian Shan region in central Asia and moved along the famous Silk Road trading path, they have undergone selection for distinct phenotypic traits. In this study, a high-throughput single nucleotide polymorphism (SNP) genotyping assay is used to investigate relationships of Malus species, draw inferences on the domestication history, identify traits critical for domestication, and assess potential genetic loci under selection. A total of 160 Malus accessions, including wild species, old and new apple cultivars, and advanced selections, were genotyped. Of 1536 SNPs from GoldenGate oligonucleotide pool assays (OPAs), 901 SNPs fulfilled filtering criteria. A principal component analysis (PCA) revealed that most M. × domestica accessions grouped together. A total of 67 loci, including 13 genomic SNPs and 54 genic SNPs, have been identified as potential targets for selection during evolution of the apple genome from its wild progenitor M. sieversii. Genes introgressed from local wild species into M. × domestica are associated with adaptation to local environments, while genes for fruit quality traits are derived from M. sieversii.