The drought of 1983 resulted in some 10 billion dollars in agricultural losses and has focused attention on the vulnerability of our major crops to this devastating form of environmental stress. This article is concerned with the molecular biology of a new class of genes, called osm (osmotic tolerance) genes, that protect bacteria like Escherichia coli against osmotic stress and may work in a similar manner in plants and animals. Osm genes govern the production of a class of molecules, such as betaine and proline, that protect the cell and its constituents against dehydration. These osmoprotectant molecules have been known for many years to accumulate in plants but have only recently been shown to have potent antistress activity for bacteria.

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Background The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Findings Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Conclusion Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.

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Both sorbitol and sucrose are synthesized in source leaves and transported to fruit for supporting fruit growth in tree fruit species of the Rosaceae family. In apple (Malus domestica), antisense suppression of aldose-6-phosphate reductase, the key enzyme for sorbitol synthesis, significantly decreased the sorbitol concentration but increased the sucrose concentration in leaves, leading to a lower sorbitol but a higher sucrose supply to fruit in these plants. In response to this altered carbon supply, the transgenic fruit had lower concentration of sorbitol and much higher concentration of glucose but similar levels of fructose, sucrose, and starch throughout fruit development relative to the untransformed control. Activities of sorbitol dehydrogenase, fructokinase, and sucrose phosphate synthase were lower, whereas activities of neutral invertase, sucrose synthase, and hexokinase were higher in the transgenic fruit during fruit development. Transcript levels of MdSOT1, MdSDHs, MdFK2, and MdSPS3/6 were downregulated, whereas transcript levels of MdSUC1/4, MdSUSY1-3, MdNIV1/3, MdHKs, and MdTMT1 were upregulated in the transgenic fruit. These findings suggest that the Sucrose cycle and the sugar transport system are very effective in maintaining the level of fructose and provide insights into the roles of sorbitol and sucrose in regulating sugar metabolism and accumulation in sorbitol-synthesizing species.

Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes, which greatly complicates genome sequence assembly. The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species. We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa × J. regia using a novel combination of single-molecule sequencing and optical genome mapping technologies. The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions. Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long. The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes, many of them transcribed. Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes, which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes. Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other. The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes. Given the importance of J. microcarpa × J. regia hybrids as potential walnut rootstocks, we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution. We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.

Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera. While these are ‘draft’ genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of each reference genome to the remaining six. In addition, we have re-sequenced a sample of accessions from four Juglans species (including regia). The variation discovered in these surveys comprises a critical resource for experimentation and breeding, as well as a solid complementary annotation. To demonstrate the potential of these resources the structural and sequence variation in and around the polyphenol oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in the domestication of walnuts. The apparently Juglandaceae specific PPO1 duplicate shows accelerated divergence and an excess of amino acid replacement on the lineage leading to accessions of the domesticated nut crop species, Juglans regia and sigillata.

In plant-microbe interactions, plant sugars produced by photosynthesis are not only a carbon source for pathogens, but may also act as signals that modulate plant defense responses. Here, we report that decreasing sorbitol synthesis in apple () leaves by antisense suppression of () leads to downregulation of 56 () genes and converts the phenotypic response to from resistant to susceptible. We identified a resistance protein encoded by the apple gene and a small protein encoded by the fungal gene that interact in both a yeast two-hybrid assay and a bimolecular fluorescence complementation assay. Deletion of in enables gain of virulence on the wild-type control plant. Overexpression of in two antisense lines increases resistance, whereas RNAi suppression of in the wild-type control decreases resistance against MdWRKY79 transcriptionally regulates by binding to the promoter of in response to sorbitol, and exogenous sorbitol feeding partially restores resistance of the antisense lines to These findings indicate that sorbitol modulates resistance to via the MdNLR16 protein that interacts with the fungal effector in a classic gene-for-gene manner in apple.