European pears (Pyrus communis L.) require a range of cold-temperature exposure to induce ethylene biosynthesis and fruit ripening. Physiological and hormonal responses to cold temperature storage in pear have been well characterized, but the molecular underpinnings of these phenomena remain unclear. An established low-temperature conditioning model was used to induce ripening of ‘D’Anjou’ and ‘Bartlett’ pear cultivars and quantify the expression of key genes representing ripening-related metabolic pathways in comparison to non-conditioned fruit. Physiological indicators of pear ripening were recorded, and fruit peel tissue sampled in parallel, during the cold-conditioning and ripening time-course experiment to correlate gene expression to ontogeny. Two complementary approaches, Nonparametric Multi-Dimensional Scaling and efficiency-corrected 2-(ΔΔCt), were used to identify genes exhibiting the most variability in expression. Interestingly, the enhanced alternative oxidase (AOX) transcript abundance at the pre-climacteric stage in ‘Bartlett’ and ‘D’Anjou’ at the peak of the conditioning treatments suggests that AOX may play a key and a novel role in the achievement of ripening competency. There were indications that cold-sensing and signaling elements from ABA and auxin pathways modulate the S1-S2 ethylene transition in European pears, and that the S1-S2 ethylene biosynthesis transition is more pronounced in ‘Bartlett’ as compared to ‘D’Anjou’ pear. This information has implications in preventing post-harvest losses of this important crop.

Physiological studies have characterized the conditioning requirements for a range of European pear cultivars under defined conditioning temperatures, exogenous ethylene application regimes, and other pre-harvest treatments 8-11. While exogenous ethylene treatment reduces cold conditioning needs, in most European pear cultivars it does not entirely supplant the need for cold conditioning. This indicates that cold-dependent mechanisms are partly responsible for regulating the development of ripening competency, which in turn impacts the quality and marketability of pear fruit. Interestingly, in contrast to P. communis and P. bretschneideri, many Japanese pear (Pyrus pyrifolia L.) varieties have no conditioning requirements and are also regarded as non-climacteric fruits because they do not display the characteristic S1 to S2 transition during ripening 12. Additionally, 'Bosc' , unique from other European pear cultivars, acquires competency for ripening with exogenous ethylene only, needing no chilling to ripen 8. Requirement of cold exposure in pear to induce ripening is reminiscent of other natural cold temperature-dependent developmental phenomena, such as the vernalization and stratification that are needed for flowering and seed germination, respectively. The genes that regulate vernalization and stratification have been well-studied in model organisms, including Arabidopsis, wheat, and barley 13-15 ; however, similar gene homologues have not yet been reported in cold-induced fruit ripening. With respect to flowering, the process of developmental initiation following an environmentally governed dormant state is known as endodormancy release 16. Thus far, endodormancy release has not been used to characterize ripening after chilling, although the two processes share many similarities with regards to the timing and environmental nature of cold required, suggesting that similar genetic and regulatory mechanisms may govern these processes. Various forms of the chilling requirement for ripening have been described in avocado and mango, although to a lesser degree than in pear, as the former are more prone to chilling injury 17,18. Few recent studies have utilized a transcriptomics approach to characterize the molecular underpinnings of cold-induced S1 to S2 transition in pear. A complex interaction of genes is involved in regulating phytohormones, secondary messengers, signaling pathways, respiration and chromatin modification that underlies cold-induced progression of ripening 19-23. Genes associated with phytohormones such as abscisic acid (ABA), auxin, and jasmonic acid, along with several transcription factors were implicated in low-temperature-mediated enhancement of ripening in 'Bartlett' 21. In 'Passe Crassane, ' the impact of low temperature-induced ethylene (LT) and the effects of exogenous ethylene treatments were evaluated using a transcriptomics approach 24. It was observed that the expression of a subset of the LT-induced differentially expressed genes was disrupted by 1-MCP treatment, indicating that ...

European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed established cold temperature conditioning treatments for ripening of two pear cultivars, 'D'Anjou' and 'Bartlett'. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four different developmental stages during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.For both cultivars, fruit softening accelerated once the fruit was transferred to 20°C. The rate of softening was more rapid for 'Bartlett' than 'D'Anjou'. RNAseq Assembly AnalysisRNAseq assembly generated 140077 contigs (Supplementary File 1). In the OmicsBox suite, the maSigPro R package was used to conduct time course differential expression analyses for both cultivars. 17,711 differentially expressed contigs (p<0.05) were identified for 'D'Anjou', with 7,174 of these contigs exhibiting significant linear or quadratic trends over time (R>0.8). In 'Bartlett' 31,481 contigs were identified as being differentially expressed, with 7,174 contigs exhibiting significant quadratic or linear trends over time (R>0.8) (Supplementary File 2). Similarities and differences in expression trends of contigs of interest between 'D'Anjou' and 'Bartlett', as well as expression patterns of differentially expressed contigs (DECs) associated with ethylene and phytohormone metabolism, abscisic acid metabolism, TCA cycle, respiration, were assessed. Additionally, in order to better understand the mechanisms underlying the chilling requirement for ripening in Pyrus, the expression of genes associated with: vernalization, flowering, dormancy, and other processes directly induced by cold/chilling were observed. Preclimacteric expression of AOX1 peaked during conditioning prior to onset of ripening (Figure 1), supporting the hypothesis. Additional key genes, including those that mediate vernalization and endodormancy release were also observed to be differentially expressed. Detailed analysis of RNAseq results and enriched gene ontologies related to phytohormone metabolism and coldresponse pathways are discussed in detail in the following sections.

Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. 'Oregon Spring' grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.Significance statement: Organic fertilizer changes the expression of the tomato genome, induces photosynthetic stress which elicits higher production of secondary metabolites.

Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. 'Oregon Spring' grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.

The codling moth, Cydia pomonella, is a worldwide pest of pome fruits. Neuropeptides regulate most physiological functions in insects and represent new targets for the development of control agents. The only neuropeptides reported from the codling moth to date are the allatostatin A family peptides. To identify other neuropeptides and peptide hormones from codling moth, we analyzed head transcriptomes, identified 50 transcripts, and predicted 120 prepropeptides for the codling moth neuropeptides and peptide hormones. All transcripts were amplified, and these sequences were verified. One of the notable findings in this study is that diapause hormones (DHs) reported from Tortricid moths, including the codling moth, do not have the WFGPRL sequence in C‐terminal ends in the pban genes. The C‐terminal motif is critical to characterize insect DH peptides, and always conserved in pban/dh genes in Lepidoptera and many insect orders. Interestingly, the WFGPRL sequence was produced only from the capa gene in the codling moth. The allatostatin A‐family encoding transcript predicted nine peptides, seven of which, as expected, are identical to those previously isolated from the moth. We also identified new codling moth orthologs of insect neuropeptides including CCHamides, allatostatin CC, RYamides, and natalisins. The information provided in this study will benefit future codling moth investigations using peptidoproteomics to determine peptide presence and functions.

Cultivars of the same species exhibit a large degree of variation in fruit quality traits, which can be directly influenced by differences in gene expression due to allelic variations and interactions with the environment. For Malus × domestica Borkh. (apple), fruit quality traits, including color, texture, aroma, flavor profile, and shelf life, are of utmost economic importance. In order to identify genes potentially influencing these traits, a direct comparative transcriptome profiling approach, based on the differential display technique, was performed using "Golden Delicious" and "Honeycrisp" apple endocarp and peel tissues. A total of 45 differentially expressed sequence tags were identified between the two apple varieties. Reanalysis of a previously published fruit developmental microarray expression experiment revealed that only one of the 45 sequence tags was represented on the array. Differential expression of 31 sequence tags from the peel tissue was validated using quantitative reverse transcription PCR, confirming the robustness of the differential display approach to quickly identify differentially expressed sequence tags. Among these were genes annotated to be involved in ripening, phytohormone signaling, transcription factors, and fruit texture. This work demonstrates yet again the utility of the differential display technique to rapidly identify genes related to desirable traits.

We report here draft whole genome sequences of three novel strains of Photorhabdus luminescens of 5.2–5.3 Mbps in size, and with a G + C content of 42.5% (each). Symbiotic γ-proteobacteria belonging to the genera, Photorhabdus (Family: Enterobacteriaceae) with their natural vectors, the entomopathogenic nematodes (EPN) (Phylum: Nematoda; Order: Rhabditida; Family: Heterorhabditidae), have emerged as important biological control agents of insect pests, and are capable of production and delivery of diverse compounds to influence host biology [1], [2], [3]. Analysis of these genomes is expected to provide enhanced insight into mechanisms of virulence, insecticidal toxin genetic diversity, antibiotic resistance and monoxenicity. The nucleotide sequence information for the three strains NBAII PLHb105, NBAII HiPL101 and NBAII H75HRPL105 has been deposited in NCBI Nucleotide database and is accessible via AZAB00000000, JTHJ00000000 and JXUR00000000 accession numbers respectively.