BackgroundPear (Pyrus) is a globally grown fruit, with thousands of cultivars in five domesticated species and dozens of wild species. However, little is known about the evolutionary history of these pear species and what has contributed to the distinct phenotypic traits between Asian pears and European pears.ResultsWe report the genome resequencing of 113 pear accessions from worldwide collections, representing both cultivated and wild pear species. Based on 18,302,883 identified SNPs, we conduct phylogenetics, population structure, gene flow, and selective sweep analyses. Furthermore, we propose a model for the divergence, dissemination, and independent domestication of Asian and European pears in which pear, after originating in southwest China and then being disseminated throughout central Asia, has eventually spread to western Asia, and then on to Europe. We find evidence for rapid evolution and balancing selection for S-RNase genes that have contributed to the maintenance of self-incompatibility, thus promoting outcrossing and accounting for pear genome diversity across the Eurasian continent. In addition, separate selective sweep signatures between Asian pears and European pears, combined with co-localized QTLs and differentially expressed genes, underline distinct phenotypic fruit traits, including flesh texture, sugar, acidity, aroma, and stone cells.ConclusionsThis study provides further clarification of the evolutionary history of pear along with independent domestication of Asian and European pears. Furthermore, it provides substantive and valuable genomic resources that will significantly advance pear improvement and molecular breeding efforts.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1452-y) contains supplementary material, which is available to authorized users.

BackgroundWRKY transcription factors (TFs) constitute one of the largest protein families in higher plants, and its members contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. WRKY proteins play significant roles in plant development, and in responses to biotic and abiotic stresses. Pear (Pyrus bretschneideri) is one of the most important fruit crops in the world and is frequently threatened by abiotic stress, such as drought, affecting growth, development and productivity. Although the pear genome sequence has been released, little is known about the WRKY TFs in pear, especially in respond to drought stress at the genome-wide level.ResultsWe identified a total of 103 WRKY TFs in the pear genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the pear WRKY (PbWRKY) family was classified into seven groups (Groups 1, 2a–e, and 3). The microsyteny analysis indicated that 33 (32 %) PbWRKY genes were tandemly duplicated and 57 genes (55.3 %) were segmentally duplicated. RNA-seq experiment data and quantitative real-time reverse transcription PCR revealed that PbWRKY genes in different groups were induced by drought stress, and Group 2a and 3 were mainly involved in the biological pathways in response to drought stress. Furthermore, adaptive evolution analysis detected a significant positive selection for Pbr001425 in Group 3, and its expression pattern differed from that of other members in this group. The present study provides a solid foundation for further functional dissection and molecular evolution of WRKY TFs in pear, especially for improving the water-deficient resistance of pear through manipulation of the PbWRKYs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2233-6) contains supplementary material, which is available to authorized users.

NAC (NAM, ATAF, and CUC) transcription factors are important regulator in abiotic stress and plant development. However, knowledge concerning the functions of plant NAC TFs functioning in stress tolerance and the underlying molecular basis are still limited. In this study, we report functional characterization of the NAC TF, PbeNAC1, isolated from Pyrus betulifolia. PbeNAC1 were greatly induced by cold and drought, while salt stress had little effect on expression. PbeNAC1 was localized in the nuclei showed transactivation activity. Overexpression of PbeNAC1 conferred enhanced tolerance to multiple stresses, including cold and drought, as supported by lower levels of reactive oxygen species, higher survival rate, higher activities of enzymes, relative to wild-type (WT). In addition, steady-state mRNA levels of 15 stress-responsive genes coding for either functional or regulatory proteins were higher levels in the transgenic plants relative to the WT with drought or cold treatment. yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that PbeNAC1 protein can physically interact with PbeDREB1 and PbeDREB2A. Taken together, these results demonstrate that pear PbeNAC1 plays an important role in improving stress tolerance, possibly by interacting with PbeDREB1 and PbeDREB2A to enhance the mRNA levels of some stress-associated genes.

With an extension of the absorption band toward visible light, plasmonic photocatalysts directly harvest energy from solar light without compromising the activity, offering a desirable way to address energy and environmental issues. Here we demonstrate photocatalytic oxidation of formaldehyde in air over plasmonic Au/TiO 2 catalyst under visible light in a single-pass continuous flow reactor. Compared to that under dark, a significant enhancement of up to 5 times the reaction rate at 13% RH under visible light is achieved. Au/TiO 2 catalyst exhibits very high activity, a complete conversion of formaldehyde of 83.3% under visible light at 44% RH, but is completely inactive in dry air even under visible light. Also, the plasmonic Au/TiO 2 is efficient for photocatalytic oxidation of formaldehyde under visible light, which is evidenced by a slight difference of conversion between UV light and visible light. To disclose the underlying mechanism, in situ diffuse reflectance infrared Fourier transform (DRIFT) spectra studies are conducted. The contributions of TiO 2 and Au (supported on TiO 2 ), moisture, and visible light are identified. It is ascertained that moisture is indispensable to carbonate decomposition and also accelerates dioxymethylene (DOM) oxidation to formate. Visible light enhances the rate-determining steps of formate oxidation to carbonate and carbonate decomposition. It appropriately illustrates the remarkable difference in activities. On the basis of the spectra experiments, such a pathway of formaldehyde oxidation is proposed, which undergoes four sequential reaction steps (k 1 , k 2 , k 3 , k 4 ) with reaction conditions dependent on moisture and visible light over Au/TiO 2 catalyst. On the basis of the approximately identical spectra, which indicate the same reaction pathways under visible light or under dark, the insights into the mechanism for photocatalytic oxidation of formaldehyde in air under visible light over Au/TiO 2 , are obtained.

Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants.