A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing

Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus 'Aili' at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in 'Aili' and previously published 'Francesco' and 'Scarlet Queen'. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.

Melatonin strongly enhances the Agrobacterium- mediated transformation of carnation in nitrogen-depleted media

With the rising demand for new cultivars of carnation, efficient transformation protocols are needed to enable the bioengineering of new traits. Here, we established a novel and efficient Agrobacterium-mediated transformation system using callus as the target explant for four commercial carnation cultivars. Leaf-derived calli of all cultivars were inoculated with Agrobacterium tumefaciens strain LBA4404 containing the plasmid pCAMBIA 2301 harboring genes for β-glucuronidase (uidA) and neomycin phosphotransferase (nptII). Polymerase chain reaction (PCR) and histochemical assays confirmed the presence of uidA and β-glucuronidase (GUS), respectively in transgenic shoots. The effect on transformation efficiency of medium composition and the presence of antioxidants during inoculation and co-cultivation was investigated. The transformation efficiency was increased in Murashige and Skoog (MS) medium lacking KNO₃ and NH₄NO_3, and also in MS medium lacking macro and micro elements and Fe to 5% and 3.1% respectively, compared to 0.6% in full-strength medium. Transformation efficiency was increased dramatically to 24.4% across all carnation cultivars by the addition of 2 mg/l melatonin to nitrogen-depleted MS medium. Shoot regeneration was also doubled in this treatment. The establishment of this efficient and reliable transformation protocol can advance the development of novel carnation cultivars through molecular breeding approaches.

Efficacy of Syzygium aromaticum essential oil on the growth and enzymatic activity of pathogenic Candida albicans strains

BACKGROUND AND PURPOSE

Candida albicans (C. albicans) is the most common human pathogen owing to the most virulence factors. It seems that extracellular hydrolytic enzymes play a key role in C. albicans pathogenicity. The present study aimed to assess the susceptibility and enzymatic activity of pathogenic C. albicans isolates exposed to the Syzygium aromaticum (S. aromaticum) essential oil.

MATERIALS AND METHODS

S. aromaticum oil was characterized using gas chromatography-mass spectrometry (GC-MS). The broth microdilution technique (CLSI, M27-A3) was used to determine the minimum inhibitory concentration (MIC) of test compounds. Furthermore, before and after treatment with S. aromaticum essential oil, the yeasts were analyzed regarding the proteinase (Prz), hemolysin (Hz), and phospholipase (Phz) production/activity.

RESULTS

β-caryophyllene (12.76%) was found to be the major constituent in the essential oil after eugenol (84.64%). Only one isolate of C. albicans showed the antifungal resistance to fluconazole. All isolates were susceptible to S. aromaticum essential oil with MIC of 625-1250 μg/ml. S. aromaticum oil represented the best antifungal effect against C. albicans at MIC 1000 μg/ml. The mean±SD enzyme activity of C. albicans not exposed to S. aromaticum essential oil was obtained at 0.55±0.03, 0.73±0.04, and 0.61±0.05 for proteinase, hemolysin, and phospholipase, respectively. The activities of these enzymes were reduced significantly (P<0.05) to 0.33±0.06, 0.40±0.04, and 0.16±0.03 for phospholipase, proteinase, and hemolysin, respectively, after the yeasts were subjected to S. aromaticum essential oil.

CONCLUSION

The present study aimed to determine the ability of S. aromaticum essential oil to prevent the growth of C. albicans and decrease their enzymatic activity. As a natural antifungal agent, S. aromaticum can be utilized in pharmaceutical systems.

Flavonoid biosynthesis in Dianthus caryophyllus L. is early regulated during interaction with Fusarium oxysporum f. sp. dianthi

Rooted cuttings from two carnation (Dianthus caryophyllus L.) cultivars showing contrasting responses to the vascular wilt caused by Fusarium oxysporum f. sp. dianthi (Fod) were inoculated with this phytopathogen, and some of the biochemical responses associated with flavonoid biosynthesis were investigated in the roots. The resistant cultivar ('Golem') showed a significant increase in the levels of phenolic and flavonoid compounds at 48-96 h post-inoculation (hpi) (α = 0.05). LC-MS-based analysis indicated that the flavonoids mainly included flavanol-type glycosides, especially quercetin and kaempferol aglycones. Quantification of the mRNA levels of genes encoding CHS (Chalcone Synthase), CHI (Chalcone Isomerase), FLS (Flavonol Synthase), and the transcription factor MYB11 by using reverse transcription quantitative polymerase chain reaction (RT-qPCR) indicated that the resistant cultivar exhibited higher expression levels of these genes and, therefore, showed more flavonoid accumulation at 96 hpi. The differences in the temporal regulation of the assessed variables during infection support the idea that the early expression of enzymes of the flavonoid biosynthesis pathway in carnation roots is linked to a resistance response to the hemibiotrophic pathogen Fod race 2. The present experimental approach is the first report describing the molecular mechanisms underlying flavonoid biosynthesis in carnation roots during their interaction with Fod.

Mycelium Dispersion from Fusarium oxysporum f. sp. dianthi Elicits a Reduction of Wilt Severity and Influences Phenolic Profiles of Carnation (Dianthus caryophyllus L.) Roots

The fungal pathogen Fusarium oxysporum f. sp. dianthi (Fod) is the causal agent of the vascular wilt of carnation (Dianthus caryophyllus L.) and the most prevalent pathogen in the areas where this flower is grown. For this reason, the development of new control strategies against Fod in carnation has been continuously encouraged, in particular those based on the implementation of plant resistance inducers that can trigger defensive responses to reduce the disease incidence, even at lower economical and environmental cost. In the present study, the effect of the soil supplementation of a biotic elicitor (i.e., ultrasound-assisted dispersion obtained from Fod mycelium) on disease severity and phenolic-based profiles of roots over two carnation cultivars was evaluated. Results suggest that the tested biotic elicitor, namely, eFod, substantially reduced the progress of vascular wilting in a susceptible cultivar (i.e., ‘Mizuki’) after two independent in vivo tests. The LC-MS-derived semi-quantitative levels of phenolic compounds in roots were also affected by eFod, since particular anthranilate derivatives, conjugated benzoic acids, and glycosylated flavonols were upregulated by elicitation after 144 and 240 h post eFod addition. Our findings indicate that the soil-applied eFod has an effect as a resistance inducer, promoting a disease severity reduction and accumulation of particular phenolic-like compounds.

Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Sucrose plays crucial roles in growth and responses of plants to the environment, including those in ornamental species. During post-harvest handling of cut flowers, sucrose degradation is an essential process of inter- and intra-cellular carbon partitioning affecting flower opening and senescence and, subsequently, flower quality. However, complete information about the molecular basis of sucrose degradation in ornamental flowers, which can be catalyzed by two kinds of sucrolytic enzymes, invertase (INV), and sucrose synthase (SUS), is not available from past reports. The present study shows that sucrose treatment of carnation (Dianthus caryophyllus L.) florets increased starch content in petals, accompanied by decreased vacuolar INV (VIN) activity and increased SUS activity. However, hypoxic treatment of carnation florets decreased sucrose content and cell-wall INV (CWIN) activity in petals. In silico analysis using the carnation genome database identified six CWIN, three VIN, eight cytoplasmic INV (CIN), and five SUS genes. Real-time RT-PCR analysis confirmed that these genes are differentially expressed in carnation petals in response to sucrose and hypoxic treatments, partially corresponding to the changes in enzyme activities. In contrast to DcSUS1 (Dca4507.1), a SUS gene already reported in carnation, which showed preferential expression under aerated conditions, the expression of DcSUS2 (Dca22218.1), an undescribed carnation SUS gene, was enhanced under hypoxia similarly to an alcohol dehydrogenase gene DcADH1 (Dca18671.1). These results suggest that sugar metabolism in carnation petals is regulated in response to environmental cues, accompanied by modulated activities and gene expression of a set of sucrolytic enzymes.

Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus)

Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.

Structural characteristic and phylogenetic analysis of the complete chloroplast genome of Dianthus Caryophyllus

Chloroplast genomes are widely used in genetic engineering, molecular marker development, and phylogeny. In order to analyze the complete chloroplast genome of Dianthus caryophyllus, the complete chloroplast genome of D. caryophyllus was sequenced and annotated. On the other hand, phylogenetic analysis of the chloroplast genome of D. caryophyllus was carried out. The results showed that the whole length of the chloroplast genome of D. caryophyllus was 147,604 bp, and had a typical conserved quadripartite structure. The G and C basic content of D. caryophyllus chloroplast was 36.3%. The genome contained 83 protein-coding genes, 34 tRNA genes, and 6 rRNA genes. Among the protein-coding genes, 10 genes contain a single intron and 2 genes contain two introns. The phylogeny of D. caryophyllus indicated that the closest phylogenetic relationship was D. longicalyxanus. This study provides materials for the molecular study of D. caryophyllus may improve the carnation industry.

Enhanced Conjugation of Auxin by GH3 Enzymes Leads to Poor Adventitious Rooting in Carnation Stem Cuttings

Commercial carnation (Dianthus caryophyllus) cultivars are vegetatively propagated from axillary stem cuttings through adventitious rooting; a process which is affected by complex interactions between nutrient and hormone levels and is strongly genotype-dependent. To deepen our understanding of the regulatory events controlling this process, we performed a comparative study of adventitious root (AR) formation in two carnation cultivars with contrasting rooting performance, "2101-02 MFR" and "2003 R 8", as well as in the reference cultivar "Master". We provided molecular evidence that localized auxin response in the stem cutting base was required for efficient adventitious rooting in this species, which was dynamically established by polar auxin transport from the leaves. In turn, the bad-rooting behavior of the "2003 R 8" cultivar was correlated with enhanced synthesis of indole-3-acetic acid conjugated to aspartic acid by GH3 proteins in the stem cutting base. Treatment of stem cuttings with a competitive inhibitor of GH3 enzyme activity significantly improved rooting of "2003 R 8". Our results allowed us to propose a working model where endogenous auxin homeostasis regulated by GH3 proteins accounts for the cultivar dependency of AR formation in carnation stem cuttings.

Mutualism between Klebsiella SGM 81 and Dianthus caryophyllus in modulating root plasticity and rhizospheric bacterial density

AIMS

Dianthus caryophyllus is a commercially important ornamental flower. Plant growth promoting rhizobacteria are increasingly applied as bio-fertilisers and bio-fortifiers. We studied the effect of a rhizospheric isolate Klebsiella SGM 81 strain to promote D. caryophyllus growth under sterile and non-sterile conditions, to colonise its root system endophytically and its impact on the cultivatable microbial community. We identified the auxin indole-3-acetic acid (IAA) production of Klebsiella SGM 81 as major bacterial trait most likely to enhance growth of D. caryophyllus.

METHODS

ipdC dependent IAA production of SGM 81 was quantified using LC-MS/MS and localised proximal to D. caryophyllus roots and correlated to root growth promotion and characteristic morphological changes. SGM 81 cells were localised on and within the plant root using 3D rendering confocal microscopy of gfp expressing SGM 81. Using Salkowski reagent IAA production was quantified and localised proximal to roots in situ. The effect of different bacterial titres on rhizosphere bacterial population was CFU enumerated on nutrient agar. The genome sequence of Klebsiella SGM 81 (accession number PRJEB21197) was determined to validate PGP traits and phylogenic relationships.

RESULTS

Inoculation of D. caryophyllus roots with Klebsiella SGM 81 drastically promoted plant growth when grown in agar and soil, concomitant with a burst in root hair formation, suggesting an increase in root auxin activity. We sequenced the Klebsiella SGM 81 genome, identified the presence of a canonical ipdC gene in Klebsiella SGM 81, confirmed bacterial production and secretion of IAA in batch culture using LC-MS/MS and localised plant dependent IAA production by SGM 81 proximal to roots. We found Klebsiella SGM 81 to be a rhizoplane and endophytic coloniser of D. caryophyllus roots in a dose dependent manner. We found no adverse effects of SGM 81 on the overall rhizospheric microbial population unless supplied to soil in very high titres.

CONCLUSION

Klebsiella SGM 81 effectively improves root traits of D. caryophyllus in a dose dependent manner, likely through tryptophan dependent IAA production in the rhizoplane and potentially within the intercellular spaces of root tissue. Under optimal plant growth promoting conditions in non-sterile soil, the high total microbial titre in the rhizosphere supports a mutualistic relationship between Klebsiella SGM 81 and carnation that potentially extends to the wider rhizosphere microbiota.

Effects of extended exposure to cadmium and subsequent recovery period on growth, antioxidant status and polyamine pattern in in vitro cultured carnation

The effect of different doses of Cd (0.05, 0.1 and 0.2 mM) and subsequent period in a Cd-free medium on growth, the antioxidant status and the polyamine (PA) pattern was studied using in vitro cultured nodal segments of carnation. The Cd within the tissues increased in parallel with its concentration in the culture medium, inhibited growth, altered the concentration of some minerals and decreased the levels of pigments and the total antioxidants. However, the concentration of ascorbate (Asc) + dehydroascorbate (DHA) and the Asc redox status remained unaffected, and malondialdehyde (MDA) increased only with 0.2 mM Cd. Cd also affected PA metabolism, decreasing the total PA concentration and disturbing the relative predominance of each PA fraction. Cd exposure increased the total putrescine (Put)/(spermidine (Spd) + spermine (Spm)) ratio, and an opposite pattern was recorded during the phase in Cd-free medium. Regarding individual amines, Cd induced significant changes mainly in the free Put levels. Our results suggest that Cd produces oxidative stress and that PA (especially free Put and the total Put/(Spd+Spm) ratio), are good indicators of the stress caused by Cd.

Rooting of carnation cuttings: the auxin signal

The rooting of stem cuttings is a common vegetative propagation practice in many ornamental species. Among other signals, auxin polarly transported through the stem plays a key role in the formation and growth of adventitious roots. Unlike in other plant species, auxin from mature leaves plays a decisive role in the rooting of carnation (Dianthus caryophyllus. L) cuttings. The gene DcAUX1, which codifies an auxin influx carrier involved in polar auxin transport, has now been cloned and characterized in carnation. The expression pattern of this gene was seen to depend on the organ, the cultivar and the time of cold storage. The variations observed in its expression could be related with the rooting ability of different carnation cultivars.

Screening of Carnation Cultivars for Resistance to Meloidogyne incognita

A total of 33 carnation cultivars cultured in Korea were screened for resistance to the southern root-knot nematode, Meloidogyne incognita. Carnations were tested by either inoculating with 5,000 eggs or by transplanting into a mixture of bedding medium and soil infested with an average of 435 second-stage juveniles/300 cm(3) soil. Cultivars, Desio, Castelaro, Kappa, Rara, Izu Pink, Target, and Antalia were highly resistant to M. incognita. Twelve cultivars were moderately resistant, and the remaining 14 cultivars were susceptible. These results were similar to those obtained when the cultivars were subjected to field populations of the condition on a carnation farm.