Transcriptional profiling of Petunia seedlings reveals candidate regulators of the cold stress response

Petunias are important ornamentals with the capacity for cold acclimation. So far, there is limited information concerning gene regulation and signaling pathways related to the cold stress response in petunias. A custom-designed petunia microarray representing 24816 genes was used to perform transcriptome profiling in petunia seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d. A total of 2071 transcripts displayed differential expression patterns under cold stress, of which 1149 were up-regulated and 922 were down-regulated. Gene ontology enrichment analysis demarcated related biological processes, suggesting a possible link between flavonoid metabolism and plant adaptation to low temperatures. Many novel stress-responsive regulators were revealed, suggesting that diverse regulatory pathways may exist in petunias in addition to the well-characterized CBF pathway. The expression changes of selected genes under cold and other abiotic stress conditions were confirmed by real-time RT-PCR. Furthermore, weighted gene co-expression network analysis divided the petunia genes on the array into 65 modules that showed high co-expression and identified stress-specific hub genes with high connectivity. Our identification of these transcriptional responses and groups of differentially expressed regulators will facilitate the functional dissection of the molecular mechanism in petunias responding to environment stresses and extend our ability to improve cold tolerance in plants

Fusion primer and nested integrated PCR (FPNI-PCR): a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning

<p>Abstract</p> <p>Background</p> <p>The advent of genomics-based technologies has revolutionized many fields of biological enquiry. However, chromosome walking or flanking sequence cloning is still a necessary and important procedure to determining gene structure. Such methods are used to identify T-DNA insertion sites and so are especially relevant for organisms where large T-DNA insertion libraries have been created, such as rice and <it>Arabidopsis</it>. The currently available methods for flanking sequence cloning, including the popular <it>TAIL-PCR </it>technique, are relatively laborious and slow.</p> <p>Results</p> <p>Here, we report a simple and effective fusion primer and nested integrated PCR method (<it>FPNI-PCR</it>) for the identification and cloning of unknown genomic regions flanked known sequences. In brief, a set of universal primers was designed that consisted of various 15-16 base arbitrary degenerate oligonucleotides. These arbitrary degenerate primers were fused to the 3' end of an adaptor oligonucleotide which provided a known sequence without degenerate nucleotides, thereby forming the fusion primers (FPs). These fusion primers are employed in the first step of an integrated nested PCR strategy which defines the overall <it>FPNI-PCR </it>protocol. In order to demonstrate the efficacy of this novel strategy, we have successfully used it to isolate multiple genomic sequences namely, 21 orthologs of genes in various species of Rosaceace, 4 <it>MYB </it>genes of Rosa rugosa, 3 promoters of transcription factors of Petunia hybrida, and 4 flanking sequences of T-DNA insertion sites in transgenic tobacco lines and 6 specific genes from sequenced genome of rice and <it>Arabidopsis</it>.</p> <p>Conclusions</p> <p>The successful amplification of target products through <it>FPNI-PCR </it>verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, <it>FPNI-PCR </it>represents a more sensitive, rapid and accurate technique than the established <it>TAIL-PCR </it>and <it>hiTAIL-PCR </it>procedures.</p

Identification and characterization of class E genes involved in floral organ development in Dianthus chinensis

The SEPALLATA (SEP) gene, as a 'glue' for the 'floral quartets model', plays an important role in floral organ development by forming tetramers with class A-, B-, and C- genes. The functional differentiation of class E genes has been reported in different species. Carnation (Dianthus spp.) is a world-famous economic flower that has been extensively used in landscaping, but the roles of SEP genes in carnation are unclear. Here, we found that the class E genes of D. chinensis cultivar 'L' showed different expression patterns during floral organ primordium development by transcriptome analysis. Combined with quantitative real-time PCR, its tissue and specific stage expression patterns were also different in different subclades. In addition, a yeast two-hybrid experiment was carried out to explore the interaction patterns of class E genes with other class A-, B-, and C- genes. Only DcSEP3s and DcSEP4s proteins interacted with all three classes of A-, B-, and C- proteins, and interestingly, is that DcSEP3-1 only interacted with the DcAP1 protein of class A, while the DcSEP3-2 protein only interacted with DcFUL1. Transgenic experiments showed that overexpression of DcSEP3-2 genes in Arabidopsis resulted in early flowering, smaller rosettes, dwarfism and abnormal floral organs. The transgenic line overexpressing of DcSEP3-1 only showed an early flowering phenotype. All these results indicated that the two DcSEP3s of class E genes in D. chinensis may undergo sub-functionalization. These findings advance our understanding of the molecular mechanisms of flower development in carnation

Differences in ethylene sensitivity, expression of ethylene biosynthetic genes and vase life among carnation varieties

Carnation (Dianthus caryophyllus L.) is a typical ethylene-sensitive cut flower. Variations in carnation vase life and sensitivity to ethylene have been reported, but no detailed analysis has been performed to date. In order to investigate the ethylene sensitivity of different cut carnation varieties and study the effect of ethylene on postharvest physiological changes of different carnation varieties, 14 varieties were used to explore ethylene sensitivity, and six varieties were used to analyze the release pattern of endogenous ethylene and the expression pattern of related genes. The results showed that among the 14 carnation varieties, 'Master' had the strongest ethylene sensitivity and 'Snow White' had the weakest ethylene sensitivity. Ethylene release changes of 'Master' are the terminal ascending type, and 'Cloud Shium', 'Little Pink', 'Seashell', 'Freedom' and 'Snow White' are the similar ethylene leap type. Ethylene biosynthesis genes DcACS1 and DcACO1 of 'Master' were up-regulated the most, and DcACO1 of 'Snow White' was the least up-regulated. The transient silencing and overexpression of DcACS1 and DcACO1 were performed and it was found that transient silencing can significantly delay aging, and overexpression significantly accelerates aging. This study laid the foundation for further research on the molecular mechanism of ethylene regulation of postharvest senescence of cut flowers of carnation, and also indicated the direction for further breeding and artificial screening of new storage tolerant carnation species by gene editing technology

Taking the pulse of COVID-19: A spatiotemporal perspective

The sudden outbreak of the Coronavirus disease (COVID-19) swept across the world in early 2020, triggering the lockdowns of several billion people across many countries, including China, Spain, India, the U.K., Italy, France, Germany, and most states of the U.S. The transmission of the virus accelerated rapidly with the most confirmed cases in the U.S., and New York City became an epicenter of the pandemic by the end of March. In response to this national and global emergency, the NSF Spatiotemporal Innovation Center brought together a taskforce of international researchers and assembled implemented strategies to rapidly respond to this crisis, for supporting research, saving lives, and protecting the health of global citizens. This perspective paper presents our collective view on the global health emergency and our effort in collecting, analyzing, and sharing relevant data on global policy and government responses, geospatial indicators of the outbreak and evolving forecasts; in developing research capabilities and mitigation measures with global scientists, promoting collaborative research on outbreak dynamics, and reflecting on the dynamic responses from human societies.Comment: 27 pages, 18 figures. International Journal of Digital Earth (2020

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms

Morphological and Molecular Analyses of the Interaction between Rosa multiflora and Podosphaera pannosa

Powdery mildew disease caused by Podosphaerapannosa is the most widespread disease in global cut-rose production, as well as a major disease in garden and pot roses. In this study, the powdery mildew resistance of different wild rose varieties was evaluated. Rose varieties with high resistance and high sensitivity were used for cytological observation and transcriptome and expression profile analyses to study changes at the morphological and molecular levels during the interaction between Rosa multiflora and P. pannosa. There were significant differences in powdery mildew resistance among three R. multiflora plants; R. multiflora &lsquo;13&rsquo; had high resistance, while R. multiflora &lsquo;4&rsquo; and &lsquo;1&rsquo; had high susceptibility. Cytological observations showed that in susceptible plants, 96 and 144 h after inoculation, hyphae were observed in infected leaves; hyphae infected the leaf tissue through the stoma of the lower epidermis, while papillae were formed on the upper epidermis of susceptible leaf tissue. Gene ontology enrichment analysis showed that the differentially expressed genes that were significantly enriched in biological process functions were related to the secondary metabolic process, the most significantly enriched cellular component function was cell wall, and the most significantly enriched molecular function was chitin binding. Changes in the transcript levels of important defense-related genes were analyzed. The results showed that chitinase may have played an important role in the interactions between resistant R. multiflora and P. pannosa. Jasmonic acid and ethylene (JA/ET) signaling pathways might be triggered in the interaction between susceptible R. multiflora and P. pannosa. In the resistant R. multiflora, the salicylic acid (SA) signaling pathway was induced earlier. Between susceptible plants and resistant plants, key phenylpropanoid pathway genes were induced and upregulated after P. pannosa inoculation, demonstrating that the phenylpropanoid pathway and secondary metabolites may play important and active roles in R. multiflora defense against powdery mildew infection

Functional Conservation and Divergence of Five <i>AP1/FUL</i>-like Genes in Marigold (<i>Tagetes erecta</i> L.)

Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamily genes in Asteraceae. Here, we cloned two euAP1 clade genes TeAP1-1 and TeAP1-2, and three euFUL clade genes TeFUL1, TeFUL2, and TeFUL3 from marigold (Tagetes erecta L.). Expression profile analysis demonstrated that TeAP1-1 and TeAP1-2 were mainly expressed in receptacles, sepals, petals, and ovules. TeFUL1 and TeFUL3 were expressed in flower buds, stems, and leaves, as well as reproductive tissues, while TeFUL2 was mainly expressed in flower buds and vegetative tissues. Overexpression of TeAP1-2 or TeFUL2 in Arabidopsis resulted in early flowering, implying that these two genes might regulate the floral transition. Yeast two-hybrid analysis indicated that TeAP1/FUL proteins only interacted with TeSEP proteins to form heterodimers and that TeFUL2 could also form a homodimer. In general, TeAP1-1 and TeAP1-2 might play a conserved role in regulating sepal and petal identity, similar to the functions of MADS-box class A genes, while TeFUL genes might display divergent functions. This study provides a theoretical basis for the study of AP1/FUL-like genes in Asteraceae species

Characterization and Functional Analysis of Five MADS-Box B Class Genes Related to Floral Organ Identification in Tagetes erecta.

According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs. Yeast hybrid experiments of the B class proteins showed that TePI protein could form a homodimer and heterodimers with all the other four B class proteins TeAP3-1, TeAP3-2, TeTM6-1 and TeTM6-2. No homodimer or interaction was observed between the euAP3 and TM6 clade members. Over-expression of five B class genes of T. erecta in Nicotiana rotundifolia showed that only the transgenic plants of 35S::TePI showed altered floral morphology compared with the non-transgenic line. This study could contribute to the understanding of the function of B class genes in flower development of T. erecta, and provide a theoretical basis for further research to change floral organ structures and create new materials for plant breeding