[Cloning and functional analysis of AcFMO from onion during alliine biosynthesis].

Flavin-containing monooxygenase (FMO) is the key enzyme in the biosynthesis pathway of CSOs with sulfur oxidation. In order to explore the molecular regulatory mechanism of FMO in the synthesis of onion CSOs, based on transcriptome database and phylogenetic analysis, one AcFMO gene that may be involved in alliin synthesis was obtained, the AcFMO had a cDNA of 1 374 bp and encoded 457 amino acids, which was evolutionarily closest to the AsFMO of garlic. Real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) indicated that AcFMO was the highest in the flowers and the lowest in the leaf sheaths. The results of subcellular localization showed that the AcFMO gene product was widely distributed throughout the cell A yeast expression vector was constructed, and the AcFMO gene was ecotopically overexpressed in yeast to further study the enzyme function in vitro and could catalyze the synthesis of alliin by S-allyl-l-cysteine. In summary, the cloning and functional identification of AcFMO have important reference value for understanding the biosynthesis of CSOs in onions.

Physiological and molecular changes of onion (Allium cepa L.) seeds under different aging conditions.

BACKGROUND: Onion seeds have limited storage capacity compared to other vegetable seeds. It is crucial to identify the mechanisms that induce tolerance to storage conditions and reduce seed deterioration. To address this goal, an experiment was conducted to evaluate changes in germination, biochemical, physiological, and molecular characteristics of onion seed landraces (Horand, Kazerun landraces and Zargan cultivar) at different aging levels (control, three-days and six-days accelerated aging, and natural aging for one year). RESULTS: The findings suggest that there was an increase in glucose, fructose, total sugar, and electrolyte leakage in the Horand (HOR), Kazerun (KAZ) landraces, and Zarghan (ZAR) cultivar, with Kazerun exhibiting the greatest increase. The percentage and rate of germination of Kazerun decreased by 54% and 33%, respectively, in six-day accelerated aging compared to the control, while it decreased by 12% and 14%, respectively, in Horand. Protein content decreased with increasing levels of aging, with a decrease of 26% in Kazerun landrace at six days of aging, while it was 16% in Horand landrace. The antioxidant activities of catalase, superoxide dismutase, and glutathione peroxidase decreased more intensively in Kazerun. The expression of AMY1, BMY1, CTR1, and NPR1 genes were lower in Kazerun landraces than in Horand and Zargan at different aging levels. CONCLUSIONS: The AMY1, BMY1, CTR1, and NPR1 genes play a pivotal role in onion seed germination, and their downregulation under stressful conditions has been shown to decrease germination rates. In addition, the activity of CAT, SOD, and GPx enzymes decreased by seed aging, and the amount of glucose, fructose, total sugar and electrolyte leakage increased, which ultimately led to seed deterioration. Based on the results of this experiment, it is recommended to conduct further studies into the molecular aspects involved in onion seed deterioration. More research on the genes related to this process is suggested, as well as investigating the impact of different priming treatments on the genes expression involved in the onion seed aging process.

Changes in the expression of COI1, TIR1, and ERF1 genes and respective MiRNAs in Fusarium basal Rot-Stressed onion.

Fusarium oxysporum f.sp. cepae (FOC), as basal rot fungus, is the most detrimental pathogen causing a serious threat to onion productivity in the world. In this study, we first determined FOC tolerance in seven Iranian onion cultivars, two known international onions (Texas Early Grano and Sweet Yellow Spanish), and an Allium species related to the onion (Allium asarence) based on the infection severity. Then, a transcriptional screen was performed by comparing the transcript levels of some pathogen-responsive genes (ERF1, COI1, and TIR1) and their predicted miRNAs in the sensitive (Ghermeze Azarshahr Cv.) and the resistant (A. asarence) onions to determine key genes and their miRNAs involved in the defense responses of onions to FOC. From our results, a difference was found in the COI1 and ERF1 expression 48 h after inoculation with FOC as compared to the respective 24 and 72 h. It can be explained by either special mechanisms involved in raising energy consumption efficiency or the interactive effects of other genes in the jasmonic acid (JA) and ethylene (ET) signaling pathways. Moreover, expression analysis of the pathogen-responsive genes and their targeting miRNAs identified the miR-5629, which targets the COI1 gene as a likely key factor in conferring resistance in the FOC-resistant onion, i.e., A. asarence. However, exploring the function of the miRNA/target pair is highly recommended to deeply understand the effect of the miRNA/target pair-associated pathway in the control of A. asarense-FOC interaction.

Assessment of salt and drought stress on the biochemical and molecular functioning of onion cultivars.

BACKGROUND: Salt and drought stress are the main environmental constraints that limit onion growth and productivity. Türkiye is the fifth largest onion producer, whereas the stress conditions are increasing in the region, resulting in poor crop growth. METHODS AND RESULTS: A current study was conducted under greenhouse conditions according to a completely randomized design with factorial arrangements to evaluate the performance of onion cultivars. Plants were subjected to salt stress with an application of 750 mM NaCl and drought stress was applied by depriving plants of irrigation water for 20 days to measure biochemical and transcript changes. The antioxidant activities of the cultivars were quantified by using four different methods, i.e., 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays, cupric reducing antioxidant capacity, 2,2-Diphenyl-1-picrylhydrazyl, and ferric reducing antioxidant power (FRAP). The damage to pigments, phenolic, osmolytes, and hydrogen peroxide (H2O2) accumulation was also evaluated. Results revealed that the cultivars "Elit and Hazar" had higher H2O2, maximum damage to pigments, and least accumulation of phenolics and osmolytes under both stress conditions. The cultivar "Sampiyon" performance was better under salt stress but exhibited a poor antioxidant defensive mechanism under drought stress conditions. The remaining cultivars suggested a resilient nature with a higher accumulation of osmolytes, antioxidants and phenolics. The change in transcript levels further strengthened the response of resilient cultivars; for instance, they showed higher transcript levels of superoxide dismutase, ascorbate oxidase and transcription factors (WRKY70, NAC29). It helped alleviate the oxidative stress in tolerant cultivars and maintained the physio-biochemical functioning of the cultivars.. CONCLUSION: The results of the current study will fill the gap of missing literature in onion at biochemical and molecular levels. Additionally, resilient cultivars can effectively cope with abiotic stresses to ensure future food security.

Integrated multi-omic data and analyses reveal the response pathways of to high-temperature stress.

With the intensification of the greenhouse effect and the continuous rise of global temperature, high temperatures in summer seriously affect the growth of green onion (Allium fistulosum L.var.caespitosum Makino) and reduce its yield and quality. It is important to study the mechanism of heat tolerance in green onion for selecting and breeding new varieties with high-temperature tolerance. In this study, we used the heat-tolerant green onion variety AF60 and heat-sensitive green onion variety AF35 and measured their physiological indexes under different durations of heat stress. The results showed that high-temperature stress adversely affected the water content, protein composition and antioxidant system of green onion. In addition, a comprehensive analysis using transcriptomics and metabolomics showed that heat-tolerant green onions responded positively to heat stress by up-regulating the expression of heat shock proteins, whereas heat-sensitive green onions responded to heat stress by activating the galactose metabolic pathway and maintained normal physiological activities. This study revealed the physiological performance and high-temperature response pathways of different heat-tolerant green onion cultivars under heat stress. The results further deepen the understanding of the molecular mechanism of green onion's heat stress response.

The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023.

Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).

Chromosome-level genomes of three key Allium crops and their trait evolution.

Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.

Immune responses of the Asian onion moth, Acrolepiopsis sapporensis, and their genetic factors from RNA-Seq analysis.

A nonmodel insect, Acrolepiopsis sapporensis, has been analyzed in immune responses. The total hemocytes in the fifth instar larvae were 2.33 × 106 cells/mL. These hemocytes comprised at least five different types and different relative ratios: 47% granulocytes, 26% plasmatocytes, 11% oenocytoid, 8% prohemocytes, and 5% spherulocytes. Upon bacterial challenge, some of the hemocytes exhibited typical hemocyte-spreading behaviors, such as focal adhesion, and filopodial and lamellipodial cytoplasmic extensions. The hemocyte behaviors induced cellular immune responses demonstrated by nodule formation. In addition, the plasma collected from the immune-challenged larvae exhibited humoral immune responses by bacterial growth inhibition along with enhanced phenoloxidase enzyme activity. These cellular and humoral immune responses were further analyzed by determining the immune-associated genes from a transcriptome generated by RNA-Seq. A total of about 12 Gb sequences led to about 218,116 contigs, which were predicted to encode about 46,808 genes. Comparative expression analysis showed 8392 uniquely expressed genes in the immune-challenged larvae. Differentially expressed gene (DEG) analysis among the commonly expressed genes indicated that 782 genes were upregulated and 548 genes were downregulated in the expressions after bacterial challenge. These immune-associated genes included pattern recognition receptors, immune mediation/signaling genes, and various immune effectors. Specifically, the genetic components of the Toll, IMD, and JAK/STAT immune signaling pathways were included in the DEG database. These results demonstrate the immune responses of A. sapporensis larvae and suggest the genes associated with the immune responses in this nonmodel insect.

Enabling Population Biology Studies of Stemphylium vesicarium from Onion with Microsatellites.

Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is dominant within the foliar disease complex affecting onion production in New York (NY). The disease causes premature defoliation and significant reductions in bulb weight and quality. Foliar diseases of onion are usually managed by an intensive fungicide program, but SLB management is complicated by resistance to multiple single-site modes of action. The design of integrated disease management strategies is limited by incomplete knowledge surrounding the dominant sources of S. vesicarium inoculum. To facilitate genomic-based studies of S. vesicarium populations, nine microsatellite markers were developed. The markers were multiplexed into two PCR assays containing four and five fluorescently labeled microsatellite markers. Initial testing of the S. vesicarium isolates found the markers were highly polymorphic and reproducible with an average of 8.2 alleles per locus. The markers were used to characterize 54 S. vesicarium isolates from major NY onion production regions in 2016 (n = 27) and 2018 (n = 27). Fifty-two multilocus genotypes (MLGs) were identified between these populations. Genotypic and allelic diversities were high in both the 2016 and 2018 populations. A greater degree of genetic variation was observed within populations than between years. No distinct pattern of MLGs according to population was identified and some MLGs were closely related between 2016 and 2018. The lack of evidence for linkage among loci also was strongly suggestive of clonal populations with only minor differences between the two populations. These microsatellite markers will be a foundational resource for the testing of hypotheses surrounding the population biology of S. vesicarium and therefore informing disease management.

Genome-Wide Analysis of the BAHD Family in Welsh Onion and CER2-LIKEs Involved in Wax Metabolism.

BAHD acyltransferases (BAHDs), especially those present in plant epidermal wax metabolism, are crucial for environmental adaptation. Epidermal waxes primarily comprise very-long-chain fatty acids (VLCFAs) and their derivatives, serving as significant components of aboveground plant organs. These waxes play an essential role in resisting biotic and abiotic stresses. In this study, we identified the BAHD family in Welsh onion (Allium fistulosum). Our analysis revealed the presence of AfBAHDs in all chromosomes, with a distinct concentration in Chr3. Furthermore, the cis-acting elements of AfBAHDs were associated with abiotic/biotic stress, hormones, and light. The motif of Welsh onion BAHDs indicated the presence of a specific BAHDs motif. We also established the phylogenetic relationships of AfBAHDs, identifying three homologous genes of CER2. Subsequently, we characterized the expression of AfCER2-LIKEs in a Welsh onion mutant deficient in wax and found that AfCER2-LIKE1 plays a critical role in leaf wax metabolism, while all AfCER2-LIKEs respond to abiotic stress. Our findings provide new insights into the BAHD family and lay a foundation for future studies on the regulation of wax metabolism in Welsh onion.

A scoping review of recent advances in the application of comet assay to Allium cepa roots.

The comet assay is a sensitive method for the evaluation of DNA damages and DNA repair capacity at single-cell level. Allium cepa is a well-established plant model for toxicological studies. The aim of this scoping review was to investigate the recent application of the comet assay in Allium cepa root cells to assess the genotoxicity. To explore the literature a search was performed selecting articles published between January 2015 and February 2023 from Web of Science, PubMed, and Scopus databases using the combined search terms "Comet assay" and "Allium cepa". All the original articles that applied the comet assay to Allium cepa root cells were included. Of the 334 records initially found, 79 articles were identified as meeting the inclusion criteria. Some studies reported results for two or more toxicants. In these cases, the data for each toxicant were treated separately. Thus, the number of analyzed toxicants (such as chemicals, new materials, and environmental matrices) was higher than the number of selected papers and reached 90. The current use of the Allium-comet assay seems to be directed towards two types of approach: the direct study of the genotoxicity of compounds, mainly biocides (20% of analyzed compounds) and nano- and microparticles (17%), and assessing a treatment's ability to reduce or eliminate genotoxicity of known genotoxicants (19%). Although the genotoxicity identified by the Allium-comet assay is only one piece of a larger puzzle, this method could be considered a useful tool for screening the genotoxic potential of compounds released into the environment.

Leaf cuticular waxes of wild-type Welsh onion (Allium fistulosum L.) and a wax-deficient mutant: Compounds with terminal and mid-chain functionalities.

Plant cuticles cover aerial organs to limit non-stomatal water loss and protect against insects and pathogens. Cuticles contain complex mixtures of fatty acid-derived waxes, with various chain lengths and diverse functional groups. To further our understanding of the chemical diversity and biosynthesis of these compounds, this study investigated leaf cuticular waxes of Welsh onion (Allium fistulosum L.) wild type and a wax-deficient mutant. Leaf waxes were extracted with chloroform, separated using thin layer chromatography (TLC), and analyzed using gas chromatography-mass spectrometry (GC-MS). The extracts contained typical wax compound classes found in nearly all plant lineages but also two uncommon compound classes. Analyses of characteristic MS fragmentation patterns followed by comparisons with synthetic standards identified the latter as very-long-chain ketones and primary ketols. The ketols were minor compounds, with chain lengths ranging from C28 to C32 and carbonyls mainly on C-18 and C-20 in wild type wax, and a C28 chain with C-16 carbonyl in the mutant. The ketones made up 70% of total wax in the wild type, consisting mainly of C31 isomers with carbonyl group on C-14 or C-16. In contrast, the mutant wax comprised only 4% ketones, with chain lengths C27 and C29 and carbonyls predominantly on C-12 and C-14, respectively. A two-carbon homolog shift between wild type and mutant was also observed in the primary alcohols (a major wax compound class), whilst alkanes exhibited a four-carbon shift. Overall, the compositional data shed light on possible biosynthetic pathways to wax ketones that can be tested in future studies.

The Control of the Crossover Localization in Allium.

Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F1 diploid (2n = 2x = 8C + 8F) and F1 triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F1 hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F1 triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F1 diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F1 diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F1 diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F1 triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed.

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.

BACKGROUND: The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer. RESULTS: SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation. CONCLUSION: Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.

Identification, cloning and characterization of AcMSH1 from Onion (Allium cepa L.).

BACKGROUND: MSH1 (MutS homolog1) is a nuclear-encoded protein that plays a crucial role in maintaining low mutation rates and stability of the organellar genome. While plastid MSH1 maintains nuclear epigenome plasticity and affects plant development patterns, mitochondrial MSH1 suppresses illegitimate recombination within the mitochondrial genome, affects mitochondrial genome substoichiometric shifting activity and induces cytoplasmic male sterility (CMS) in crops. However, a detailed functional investigation of onion MSH1 has yet to be achieved. MATERIALS AND RESULTS: The homology analysis of onion genome database identified a single copy of the AcMSH1 gene in the onion cv. Bhima Super. In silico analysis of AcMSH1 protein sequence revealed the presence of 6 conserved functional domains including a unique MSH1-specific GIY-YIG endonuclease domain at the C-terminal end. At N-terminal end, it has signal peptide sequences targeting chloroplast and mitochondria. The concentration of AcMSH1 was found to be highest in isolated mitochondria, followed by chloroplasts, and negligible in the cytoplasmic fraction; which proved its localization to the mitochondria and chloroplasts. Quantitative expression analysis revealed that AcMSH1 protein levels were highest in leaves, followed by flower buds, root tips, flowers, and umbels, with the lowest amount found in callus tissue. CONCLUSION: Onion genome has single copy of MSH1, with characteristic GIY-YIG endonuclease domain. AcMSH1 targeted towards both chloroplasts and mitochondria. The identification and characterisation of AcMSH1 may provide valuable insights into the development of CMS lines in onion.

Three Glycosyltransferase Mutants in a One-Pot Multi-enzyme System with Enhanced Efficiency for Biosynthesis of Quercetin-3,4'-O-diglucoside.

Quercetin-3,4'-O-diglucoside (Q3,4'G), among the major dietary flavonoids, is superior to quercetin aglycone or quercetin monoglucoside in solubility. However, its low content in nature makes it hard to be prepared in large quantities by traditional extraction methods. In the present study, the F378S mutant of UGT78D2 (78D2_F378S) derived from Arabidopsis thaliana with improved regioselectivity and the V371A mutant of UGT73G1 (73G1_V371A) derived from Allium cepa were adopted to realize a two-step continuous glycosylation of quercetin to produce Q3,4'G. The mutation S31D was introduced to the sucrose synthase from Micractinium conductrix with enhanced activity, which was responsible for regenerating UDP-glucose by coupling with 78D2_F378S and 73G1_V371A. Using the aforementioned enzymes, prepared from the three-enzyme co-expression strain, 4.4 ± 0.03 g/L (7.0 ± 0.05 mM, yield 21.2%) Q3,4'G was produced from 10 g/L quercetin after reaction for 24 h at 45 °C.

Mitochondrial genetic diversity of Thrips tabaci (Thysanoptera: Thripidae) in onion growing regions of the United States.

Onion thrips (Thrips tabaci Lindeman, Thysanoptera: Thripidae) causes severe damage to many horticultural and agronomic crops worldwide. It also acts as a vector of several plant viruses. T. tabaci is a key pest of Allium cepa in the United States. However, there is limited information available on the genetic variation within and between T. tabaci populations in the United States and its key evolutionary parameters. In the current study, 83 T. tabaci specimens were collected from A. cepa from 15 different locations comprising four states of the United States. A total of 92 mtCOI gene sequences of T. tabaci from A. cepa were analyzed to understand the genetic diversity and structure of T. tabaci collected from onion host. Seven distinct haplotypes of T. tabaci infesting A. cepa were identified from the current collection, while nine T. tabaci sequences retrieved from GenBank comprised 5 haplotypes. Overall, 15 haplotypes of T. tabaci infesting A. cepa were identified in the world that includes the ten haplotypes in the United States. In the phylogenetic analysis, all the populations collected during the study clustered with thelytokous lineage, while T. tabaci sequences retrieved from GenBank corresponded to leek-associated arrhenotokous lineage. The highest genetic variation was found in Elba and Malheur populations with 3 haplotypes identified in each. The results suggest that haplotypes 1 and 7 are more frequently prevailing haplotypes in the north-western United States, with haplotype 1 being the predominant all over the country. The eastern United States appears to have a more diverse group of haplotypes. The populations from Hungary constituted distinct haplotypes and a haplotype from Kingston linked it with the predominant haplotype.

A novel deltacryptic virus identified in Allium cepa from Brazil.

 This work describes a novel partitivirus genome assembled from RNA-seq data generated from onion tissue from fields in Brazil. A new partitivirus genome composed of three dsRNAs, which was closely related to arhar cryptic virus 1, was assembled from Allium cepa samples from Brazil. The genomic sequences were also identified from available transcriptomic datasets of onion samples from China, Czech Republic, India, South Korea and USA. According to the species demarcation in the Partitiviridae family, the new virus was classified into the genus Deltapartitivirus with the suggested name of allium deltapartitivirus. This is the first report of the occurrence of a cryptic virus in plants of the genus Allium, and therefore, this work contributes to the understanding of the genetic diversity of partitiviruses  that infect the genus Allium. Keywords: Allium sp.; high-throughput sequencing; partitiviruses.

Cloning and Expression Analysis of Onion (Allium cepa L.) MADS-Box Genes and Regulation Mechanism of Cytoplasmic Male Sterility.

Flower organ development is one of the most important processes in plant life. However, onion CMS (cytoplasmic male sterility) shows an abnormal development of floral organs. The regulation of MADS-box transcription factors is important for flower development. To further understand the role of MADS-box transcription factors in the regulation of cytoplasmic male sterility onions. We cloned the full-length cDNA of five MADS-box transcription factors from the flowers of onion using RACE (rapid amplification of cDNA ends) technology. We used bioinformatics methods for sequence analysis and phylogenetic analysis. Real-time quantitative PCR was used to detect the expression patterns of these genes in different onion organs. The relative expression levels of five flower development genes were compared in CMS onions and wild onions. The results showed that the full-length cDNA sequences of the cloned MADS-box genes AcFUL, AcDEF, AcPI, AcAG, and AcSEP3 belonged to A, B, C, and E MADS-box genes, respectively. A phylogenetic tree construction analysis was performed on its sequence. Analysis of MADS-box gene expression in wild onion and CMS onion showed that the formation of CMS onion was caused by down-regulation of AcDEF, AcPI, and AcAG gene expression, up-regulation of AcSEP3 gene expression, and no correlation with AcFUL gene expression. This work laid the foundation for further study of the molecular mechanism of onion flower development and the molecular mechanism of CMS onion male sterility.

Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin.

Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74T (=IBSBF 3371 T = CBAS 905 T) and CCRMBC51T (=IBSBF3370T = CBAS 904 T) as type strains, respectively.