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Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding., (© 2022. The Author(s).)

Cucumber ( Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS ( gibberellic acid insensitive, repressor of GAI, and scarecrow ) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana , GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species ( A. thaliana and Solanum lycopersicum ). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS ( CsaGRAS ) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.

Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber., Competing Interests: The authors have declared that no competing interests exist.

Fourteen cucumber lines were tested for genetic homozygosity and performed pairwise comparison to identify a pair with the highest DNA polymorphic level. Cucumber accessions CSL0067 and CSL0139 were selected to generate 315 F 2 populations. The genetic linkage map based on 66 polymorphic SSR markers was constructed. It composed of eight linkage groups (LGs) spanning 474.4 cM. Downy mildew disease reaction was evaluated in cotyledons, first and second true leaf on 7, 10, and 14 day after inoculation. The results showed that downy mildew resistance was controlled by multiple recessive genes. The susceptible to resistant ratio of F 2 progenies fit 9:7 susceptible/resistant segregation types corresponding to duplicate recessive epistasis. Fourteen QTLs were detected. The phenotypic variance ranged from 5.0 to 12.5%, while LOD values ranged from 3.538 to 9.165. Two major QTLs and two QTL hotspots were identified. Moreover, the additive effects data explained that these QTL reduced downy mildew susceptibility.

Corynespora leaf spot caused by Corynespora cassiicola is one of the major diseases in cucumber ( Cucumis sativus L.). However, the resistance mechanisms and signals of cucumber to C. cassiicola are unclear. Here, we report that the mildew resistance locus O (MLO) genes, CsMLO1 and CsMLO2 , are both negative modulators of the cucumber defense response to C. cassiicola . Subcellular localization analysis showed that CsMLO1 and CsMLO2 are localized in the plasma membrane. Expression analysis indicated that the transcript levels of CsMLO1 and CsMLO2 are linked to the defense response to C. cassiicola . Transient overexpression of either CsMLO1 or CsMLO2 in cucumber cotyledons reduced resistance to C. cassiicola , whereas silencing of either CsMLO1 or CsMLO2 enhanced resistance to C. cassiicola . The relationships of pathogenesis-related proteins, reactive oxygen species (ROS)-associated genes, and abscisic acid (ABA)-related genes to the overexpression and silencing of CsMLO1 / CsMLO2 in non-infested cucumber plants were investigated. The results indicated that CsMLO1 mediated resistance against C. cassiicola by regulating the expression of pathogenesis-related proteins and ROS-associated genes, as well as through ABA signaling pathway-associated genes. The CsMLO2 -mediated resistance against C. cassiicola primarily involves regulation of the expression of pathogenesis-related proteins. Our findings will guide strategies to enhance the resistance of cucumber to corynespora leaf spot.

Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and A-16 (drought-sensitive). In our present study, combining the analysis of phenotype, twelve samples of cucumber were carried out a transcriptomic profile by RNA-Seq under normal and water-deficiency conditions, respectively. A total of 1008 transcripts were differentially expressed under normal conditions (466 up-regulated and 542 down-regulated) and 2265 transcripts under drought stress (979 up-regulated and 1286 down-regulated). The significant positive correlation between RNA sequencing data and a qRT-PCR analysis supported the results found. Differentially expressed genes (DEGs) involved in metabolic pathway and biosynthesis of secondary metabolism were significantly changed after drought stress. Several genes, which were related to sucrose biosynthesis ( Csa3G784370 and Csa3G149890 ) and abscisic acid (ABA) signal transduction ( Csa4M361820 and Csa6M382950 ), were specifically induced after 4 days of drought stress. DEGs between the two contrasting cultivars identified in our study provide a novel insight into isolating helpful candidate genes for drought tolerance in cucumber.

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the major foliar diseases prevailing in cucumber-growing areas. The mechanism of DM resistance in cucumber, particularly the plant introduction (PI) 197088 from India, is presently unclear. Quantitative trait locus (QTL) mapping is an efficient approach to studying DM resistance genes in cucumber. In this study, we performed QTL mapping for DM resistance in PI 197088 with 183 F 2 -derived F 3 (F 2:3 ) families from the cross between PI 197088 (DM resistant) and Changchunmici (DM susceptible). A linkage map was constructed using 141 simple sequence repeat markers. Phenotypic data were collected from seven independent experiments. In total, five QTL were detected on chromosomes 1, 3, 4, and 5 with DM resistance contributed by PI 197088. The QTL on chromosome 4, dm4.1, was reproducibly detected in all indoor experiments, which could explain 27% of the phenotypic variance detected. Additionally, dm1.1 and dm5.2 showed moderate effects, while dm3.1 and dm5.1 were minor-effect QTL. This study revealed the unique genetic architecture of DM resistance in PI 197088, which may provide important guidance for efficient use in cucumber breeding for DM resistance.

Background: Powdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8., Results: Whole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers. This led to the identification of a ~6.8 Mb substituted segment predicted to contain 856 genes. RNA-seq was used to study gene expression differences in PM treated (plants harvested 48 h after inoculation) and untreated (control) SSL508-28 and D8 lines. Exactly 1,248 and 1,325 differentially expressed genes (DEGs) were identified in SSL508-28 and D8, respectively. Of those, 88 DEGs were located in the ~6.8 Mb segment interval. Based on expression data and annotation, we identified 8 potential candidate genes that may participate in PM resistance afforded by Pm5.1, including two tandemly arrayed genes encoding receptor protein kinases, two transcription factors, two genes encoding remorin proteins, one gene encoding a P-type ATPase and one gene encoding a 70 kDa heat shock protein. The transcriptome data also revealed a complex regulatory network for Pm5.1-mediated PM resistance that may involve multiple signal regulators and transducers, cell wall modifications and the salicylic acid signaling pathway., Conclusion: These findings shed light on the cucumber PM defense mechanisms mediated by Pm5.1 and provided valuable information for the fine mapping of Pm5.1 and breeding of cucumber with enhanced resistance to PM.

The complete chloroplast genome sequence of wild cucumber (Cucumis sativus var. hardwickii) was determined and characterized in this study. The genome is of 155 277 bp in length, containing a pair of inverted repeats regions (IRs) of 25 198 bp, which are separated by a large single-copy region of 86 618 bp and a small single-copy region of 18 263 bp. The wild cucumber chloroplast genome has 130 known genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Among these genes, 19 comprise one or two introns. There are 11 tRNA genes present in the IR of the chloroplast genome. Phylogenomic analysis showed that C. sativus var. hardwickii forms a cluster with other Cucumis species with strong bootstrap supports and is closely related to C. sativus var. sativus. This newly sequenced chloroplast genome sequence may provide useful genetic information to explore wild cucumber germplasms for cucumber breeding programs.

The complete chloroplast genome sequence of wild cucumber (Cucumis sativus var. hardwickii) was generated by de novo assembly with low-coverage whole-genome sequence data. The 155 277 bp genome containing a pair of inverted repeats (IRs) of 25 198 bp separated by a large single-copy region of 86 618 bp and a small single-copy region of 18 263 bp. The chloroplast genome contains 130 known genes, including 89 protein-coding genes, eight rRNA genes (four kinds), and 37 tRNA genes (30 kinds). Eighteen genes are duplicated in the inverted repeat regions, 16 genes contain one intron, two genes, and one ycf contain two introns. Phylogenomic analysis showed that C. sativus var. Hardwickii is closely related to C. sativus and C. hystrix.

Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

The replicase genes of five isolates of Cucumber green mottle mosaic virus from Jiangsu, Zhejiang, Hunan and Beijing were amplificated, sequenced and analyzed. The similarities of nucleotide acid sequences indicated that 129 kD and 57 kD replicase genes of CGMMV-No. 1, CGMMV-No. 2, CGMMV-No. 3, CGMMV-No. 4 and CGMMV-No. 5 were 99.64% and 99.74%, respectively. The similarities of 129 kD and 57 kD replicase genes of CGMMV-No. 1, CGMMV-No. 3 and CGMMV-No. 4 were 99.95% and 99.94%, while they were lower between CGMMV-No. 2 and the rest of four reference sequences, just from 99.16% to 99.27% and from 99.04% to 99.18%. All reference sequences could be divided into six groups in neighbor-joining (NJ) phylogenetic trees based on the replicase gene sequences of 129 kD, 57 kD protein respectively. CGMMV-No. 1, CGMMV-No. 3 and CGMMV-No. 4 were clustered together with Shandong isolate (Accession No. KJ754195) in two NJ trees; CGMMV-No. 5 was clustered together with Liaoning isolate (Accession No. EF611826) in two NJ trees; CGMMV-No. 2 was clustered together with Korea watermelon isolate (Accession No. AF417242) in phylogenetic tree of 129 kD replicase gene of CGMMV; Interestingly, CGMMV-No. 2 was classified as a independent group in phylogenetic tree of 57 kD replicase gene of CGMMV. There were no significant hydrophobic and highly coiled coil regions on 129 kD and 57 kD proteins of tested CGMMV isolates. Except 129 kD protein of CGMMV-No. 4, the rest were unstable protein. The number of transmembrane helical segments (TMHs) of 129 kD protein of CGMMV-No. 1, CGMMV-No. 2, CGMMV-No. 3 and CGMMV-No. 5 were 6, 6, 2 and 4, respectively, which were 13, 13 and 5 on the 57 kD protein of CGMMV-No. 2, CGMMV-No. 4 and CGMMV-No. 5. The glycosylation site of 129 kD protein of tested CGMMV isolates were 2, 4, 4, 4 and 4, and that of 57 kD protein were 2, 5, 2, 5 and 2. There were difference between the disorders, globulins, phosphorylation sites and B cell antigen epitopes of 129 kD and 57 kD proteins of tested CGMMV isolates. The current results that there was no significant difference between the replicase gene sequences, it was stable and conservative for intra-species and clearly difference for inter-species. CGMMV-No. 1, CGMMV-No. 3, CGMMV-No. 4 and CGMMV-No. 5 had. a close genetic relationship with Shandong and Liangning isolates (Accession No. KJ754195 and EF611826), they are potentially originate from the same source. CGMMV-No. 2 was closer with Korea isolate. High sequence similarity of tested samples were gathered for a class in phylogenetic tree. It didn't show regularity of the bioinformatics analysis results of 129 kD and 57 kD proteins of tested CGMMV isolates. There was no corresponding relationship among the molecular phylogeny and the bioinformatics analysis of the tested CGMMV isolates.

In this study, the effects of iso-osmotic solution of Mg (NO3) 2 and NaCl on seedling growth, leaf lipid peroxidation, antioxidant enzyme activities, and osmotic adjustment substance accumulation were investigated using three cucumber cultivars with different ecotypes. Then salt tolerance was evaluated by membership function method. The results revealed that under the stress of 60 and 80 mmol x L(-1) Mg(NO3) 2 solution and its isotonic 90 and 120 mmol x L(-1) NaCl solution, the seedling traits such as height, stem diameter, leaf area, fresh and dry mass of aerial part and underground parts, and antioxidant enzymes activity were obviously decreased with the increasing concentration of Mg( NO3)2 and its isotonic NaCl in the three cucumber cultivars. Moreover, the inhibitory effects became more obvious with the increasing concentration of either Mg(NO3)2 or NaCl solution. MDA content and membrane lipid peroxidation were enhanced in cucumber seedlings. Among the three cultivars, SJ31-1 changed less than the other two cultivars regarding the reduced amplitudes of biomass, and activity of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), and the increased amplitude of MDA. In addition, Mg (NO3)2 solution inhibited seedling growth more strongly than isotonic NaCl solution did, such difference was relatively significant with increasing the concentration of solution. The contents of proline, soluble amino acids, and soluble sugars varied depending on the cucumber genotype and salt type. The increased amplitude of proline content was the largest in SJ31-1, and that of soluble sugars was the largest in Lubai 19 when growing under salt treatment. The change of these parameters in Xintaimici was in between. Soluble sugars and soluble proteins were predominant osmolytes unde NaCl stress, whereas proline and soluble proteins were main osmolytes under Mg (NO3) 2 stress. Comprehensive evaluation showed that salt tolerance of the three cucumber cultivars was in order of SJ31-1 > Xintaimici > Lubai 19.

Changes in volatile content, as well as associated gene expression and enzyme activity in developing cucumber fruits were investigated in two Cucumis sativus L. lines (No. 26 and No. 14) that differ significantly in fruit flavor. Total volatile, six-carbon (C6) aldehyde, linolenic and linoleic acid content were higher during the early stages, whereas the nine-carbon (C9) aldehyde content was higher during the latter stages in both lines. Expression of C. sativus hydroperoxide lyase (CsHPL) mirrored 13-hydroperoxide lyase (13-HPL) enzyme activity in variety No. 26, whereas CsHPL expression was correlated with 9-hydroperoxide lyase (9-HPL) enzyme activity in cultivar No. 14. 13-HPL activity decreased significantly, while LOX (lipoxygenase) and 9-HPL activity increased along with fruit ripening in both lines, which accounted for the higher C6 and C9 aldehyde content at 0-6 day post anthesis (dpa) and 9-12 dpa, respectively. Volatile compounds from fruits at five developmental stages were analyzed by principal component analysis (PCA), and heatmaps of volatile content, gene expression and enzyme activity were constructed.

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

Worldwide, the developing industry of cucumbers (Cucumis sativus L.) grown in greenhouses is threatened by damage from sucking pests, especially aphids. Among these, the melon aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is the most serious. We tested the effect of two cucumber cultivars ('Royal' and'Storm') and three vermicompost concentrations (0 [control], 20, and 30%) in field soil on the development and fecundity rates of A. gossypii, by using a randomized complete block design with four replicates as a factorial experiment. The developmental times of nymphs reared on plants grown into the three vermicompost concentrations ranged from 5.5 (0%) to 8.7 (30%) d (on Storm) and from 4.3 (0%) to 7 (30%) d (on Royal). The developmental time of melon aphid's nymphs was greatest on plants grown in the culture medium with 30% vermicompost rate and least on plants reared in the soil without vermicompost. The intrinsic rate of natural increase (r,,) of A. gossypii ranged from 0.204 d(-1) on plants grown in the soil amended with 30% vermicompost rate (on Storm seedlings) to 0.458 d(-1) on plants grown in the soil without vermicompost (on Royal seedlings). Accordingly, our findings confirm that a combination of a low level of vermicompost and a partially resistant cucumber cultivar might play an important role in managing this aphid on cucumbers in greenhouses.

Repetitive DNA sequences with variability in copy number or/and sequence polymorphism can be employed as useful molecular markers to study phylogenetics and identify species/chromosomes when combined with fluorescence in situ hybridization (FISH). Cucumis sativus has three variants, Cucumis sativus L. var. sativus, Cucumis sativus L. var. hardwickii and Cucumis sativus L. var. xishuangbannesis. The phylogenetics among these three variants has not been well explored using cytological landmarks. Here, we concentrate on the organization and distribution of highly repetitive DNA sequences in cucumbers, with emphasis on the differences between cultivar and wild cucumber. The diversity of chromosomal karyotypes in cucumber and its relatives was detected in our study. Thereby, sequential FISH with three sets of multi-probe cocktails (combined repetitive DNA with chromosome-specific fosmid clones as probes) were conducted on the same metaphase cell, which helped us to simultaneously identify each of the 7 metaphase chromosomes of wild cucumber C. sativus var. hardwickii. A standardized karyotype of somatic metaphase chromosomes was constructed. Our data also indicated that the relationship between cultivar cucumber and C. s. var. xishuangbannesis was closer than that of C. s. var. xishuangbannesis and C. s. var. hardwickii., (Copyright © 2011. Published by Elsevier Ltd.)

We investigated the effects of short-term salinity stress and spermidine application to salinized nutrient solution on polyamine metabolism and various stress defense reactions in the roots of two cucumber (Cucumis sativus L.) cultivars, Changchun mici and Jinchun No. 2. Seedlings grown in nutrient solution salinized with 50mM NaCl for 8d displayed reduced relative water content, net photosynthetic rates and plant growth, together with increased lipid peroxidation and electrolyte leakage in the roots. These changes were more marked in cv. Jinchun No. 2 than in cv. Changchun mici, confirming that the latter cultivar is more salinity-tolerant than the former. Salinity stress caused an increase in superoxide and hydrogen peroxide production, particularly in cv. Jinchun No. 2 roots, while the salinity-induced increase in antioxidant enzyme activities and proline contents in the roots was much larger in cv. Changchun mici than in cv. Jinchun No. 2. In comparison to cv. Jinchun No. 2, cv. Changchun mici showed a marked increase in arginine decarboxylase, ornithine decarboxylase, S-adenosylmethionine decarboxylase and diamine oxidase activities, as well as free spermidine and spermine, soluble conjugated and insoluble bound putrescine, spermidine and spermine contents in the roots during exposure to salinity. On the other hand, spermidine application to salinized nutrient solution resulted in alleviation of the salinity-induced membrane damage in the roots and plant growth and photosynthesis inhibition, together with an increase in polyamine and proline contents and antioxidant enzyme activities in the roots of cv. Jinchun No. 2 but not of cv. Changchun mici. These results suggest that spermidine confers short-term salinity tolerance on cucumber probably through inducing antioxidant enzymes and osmoticants.

Background: A critical analysis was made of cucurbit descriptions in Dioscorides' De Materia Medica, Columella's De Re Rustica and Pliny's Historia Naturalis, works on medicine, agriculture and natural science of the 1st century ce, as well as the Mishna and Tosefta, compilations of rabbinic law derived from the same time period together with cucurbit images dating from antiquity including paintings, mosaics and sculpture. The goal was to identify taxonomically the Mediterranean cucurbits at the time of the Roman Empire., Findings: By ancient times, long-fruited forms of Cucumis melo (melon) and Lagenaria siceraria (bottle gourd) were selected, cultivated and used as vegetables around the Mediterranean and, in addition, bottle-shaped fruits of L. siceraria were employed as vessels. Citrullus lanatus (watermelons) and round-fruited forms of Cucumis melo (melons) were also consumed, but less commonly. A number of cucurbit species, including Bryonia alba, B. dioica, Citrullus colocynthis and Ecballium elaterium, were employed for medicinal purposes. No unequivocal evidence was found to suggest the presence of Cucumis sativus (cucumber) in the Mediterranean area during this era. The cucumis of Columella and Pliny was not cucumber, as commonly translated, but Cucumis melo subsp. melo Flexuosus Group (snake melon or vegetable melon).

Background: Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis., Results: Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene., Conclusion: Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.

Hyperspectral images of cucumbers under a variety of conditions were acquired to explore the potential for the detection of chilling-induced damage in whole cucumbers. Region of interest (ROI) spectral features of chilling injured areas, resulting from chilling treatment at 0 degrees C, showed the reduction of reflectance intensity over the period at post-chilling room temperature (RT) storage. A large spectral difference between good, smooth skins and chilling-injured skins occurred in the 700-850 nm visible/near-infrared (NIR) region. Both simple band ratio algorithms and principal component analysis (PCA) were attempted to discriminate the ROI spectra of good cucumber skins from those of chilling injured ones. Results revealed that both the dual-band ratio algorithm (R(811nm)/R(756nm)) and a PCA model from a narrow spectral region of 733-848 nm can detect chilling-injured skins with a success rate of over 90%. The results also suggested that chilling injury is relatively difficult to detect at the initial post-chilling RT stage, especially during the first 0-2 days in storage, due to insignificant manifestation of chilling induced symptoms.