Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses
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ABSTRACT:
SUBMITTER: Akter N
PROVIDER: S-EPMC10954154 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Plants encounter and respond to numerous abiotic stresses during their lifetimes. These stresses are often related and could therefore elicit related responses. There are, however, relatively few detailed comparisons between multiple different stresses at the molecular level. Here, we investigated the phenotypic and transcriptomic response of cultivated sunflower (Helianthus annuus L.) seedlings to three water-related stresses (i.e., dry-down, an osmotic challenge, and salt stress), as well as a generalized low-nutrient stress. All four stresses negatively impacted seedling growth, with the nutrient stress having a more divergent response from control as compared to the water-related stresses. Phenotypic responses were consistent with expectations for growth in low-resource environments, including increased (i.e., less negative) carbon fractionation values and leaf C:N ratios, as well as increased belowground biomass allocation. The number of differentially expressed genes (DEGs) under stress was greater in leaf tissue, but roots exhibited a higher proportion of DEGs unique to individual stresses. Overall, the three water-related stresses had a more similar transcriptomic response to each other vs. nutrient stress, though this pattern was more pronounced in root vs. leaf tissue. In contrast to our DEG analyses, co-expression network analysis revealed that there was little indication of a shared response between the four stresses in despite the majority of DEGs being shared between multiple stresses. Importantly, osmotic stress, which is often used to simulate drought stress in experimental settings, had little transcriptomic resemblance to true water limitation (i.e., dry-down) in our study, calling into question its utility as a means for simulating drought.
| S-EPMC9524668 | biostudies-literature
Project description:WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.
| S-EPMC7714227 | biostudies-literature
Project description:BackgroundSunflower (Helianthus annuus L.) is widely cultured in globally tropical and subtropical regions, with better resistance to various abiotic stresses as a model crop. Despite the fact that zinc finger-homeodomain (ZF-HD) genes play an important role in responding to plant growth, development and stress resistance across the multiple species, the evolutionary history and abiotic function of the ZF-HD gene family in sunflower remain largely unexplored.ResultsIn this study, we identified 15 HaZF-HD genes (designated as HaZF1-HaZF15) in the sunflower genome, and they were divided into MIF and ZHD subfamilies. The proteins from the same group were similar in conserved motifs and domains, such as motif 1 and motif 3, constituting the ZF domain, were almost existed in 15 HaZF-HD proteins. Motif 2 (HD domain) was specifically presented in the ZHD subfamily. Collinearity analysis revealed that 5 pairs of genes with fragment duplication contributed to the expansion of HaZF-HD gene family. The analysis of cis-acting element demonstrated that the response elements related the hormone response and abiotic/biotic stress were the most prevalent, followed by plant growth and development elements. In the tissue expression profile, HaZF-HD gene family had the highest expression in leaves and floral organs. Additionally, RNA-seq and RT-qPCR analysis revealed HaZF3 responded positively in the initial stage of drought stress, whereas a prompt and significant decrease of relative expression value in response to salt stress was showed in HaZF6 and HaZF9.ConclusionsOverall, this study enhances our comprehension of the function of ZF-HD genes in positive regulation of responsiveness to abiotic stress and provide key candidate genes for sunflower stress resistance breeding.
| S-EPMC11789367 | biostudies-literature
Project description:Nucleotide Binding Site-Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants' defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.
| S-EPMC6115920 | biostudies-literature
Project description:Comparative RNA-Seq study of expression in sunflower nectaries from different lines.
2018-04-03 | GSE112583 | GEO
Project description:Sesquiterpene lactones (STL) are a subclass of isoprenoids with many known bioactivities frequently found in the Asteraceae family. In recent years, remarkable progress has been made regarding the biochemistry of STL, and today the biosynthetic pathway of the core backbones of many STLs has been elucidated. Consequently, the focus has shifted to the discovery of the decorating enzymes that can modify the core skeleton with functional hydroxy groups. Using in vivo pathway reconstruction assays in heterologous organisms such as Saccharomyces cerevisiae and Nicotiana benthamiana, we have analyzed several cytochrome P450 enzyme genes of the CYP71AX subfamily from Helianthus annuus clustered in close proximity to one another on the sunflower genome. We show that one member of this subfamily, CYP71AX36, can catalyze the conversion of costunolide to 14-hydroxycostunolide. The catalytic activity of CYP71AX36 may be of use for the chemoenzymatic production of antileukemic 14-hydroxycostunolide derivatives and other STLs of pharmaceutical interest. We also describe the full 2D-NMR assignment of 14-hydroxycostunolide and provide all 13C chemical shifts of the carbon skeleton for the first time.
| S-EPMC6778120 | biostudies-literature
Project description:This is the first complete mitochondrial genome sequence for sunflower and the first complete mitochondrial genome for any member of Asteraceae, the largest plant family, which includes over 23,000 named species. The master circle is 300,945-bp long and includes 27 protein-coding sequences, 18 tRNAs, and the 26S, 5S, and 18S rRNAs.
| S-EPMC5026442 | biostudies-literature
Project description:BackgroundRetrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations.ResultsThe RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome.ConclusionThese results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed.
| S-EPMC2805666 | biostudies-literature
Project description:Cultivated sunflower (Helianthus annuus L.) exhibits numerous phenotypic and transcriptomic responses to drought. However, the ways in which these responses vary with differences in drought timing and severity are insufficiently understood. We used phenotypic and transcriptomic data to evaluate the response of sunflower to drought scenarios of different timing and severity in a common garden experiment. Using a semi-automated outdoor high-throughput phenotyping platform, we grew six oilseed sunflower lines under control and drought conditions. Our results reveal that similar transcriptomic responses can have disparate phenotypic effects when triggered at different developmental time points. Leaf transcriptomic responses, however, share similarities despite timing and severity differences (e.g., 523 differentially expressed genes (DEGs) were shared across all treatments), though increased severity elicited greater differences in expression, particularly during vegetative growth. Across treatments, DEGs were highly enriched for genes related to photosynthesis and plastid maintenance. A co-expression analysis identified a single module (M8) enriched in all drought stress treatments. Genes related to drought, temperature, proline biosynthesis, and other stress responses were overrepresented in this module. In contrast to transcriptomic responses, phenotypic responses were largely divergent between early and late drought. Early-stressed sunflowers responded to drought with reduced overall growth, but became highly water-acquisitive during recovery irrigation, resulting in overcompensation (higher aboveground biomass and leaf area) and a greater overall shift in phenotypic correlations, whereas late-stressed sunflowers were smaller and more water use-efficient. Taken together, these results suggest that drought stress at an earlier growth stage elicits a change in development that enables greater uptake and transpiration of water during recovery, resulting in higher growth rates despite similar initial transcriptomic responses.
| S-EPMC10253505 | biostudies-literature
Project description:Background: Respiratory allergy triggered by pollen allergens is increasing at an alarming rate worldwide. Sunflower pollen is thought to be an important source of inhalant allergens. Present study aims to identify the prevalence of sunflower pollinosis among the Indian allergic population and characterizes the pollen allergens using immuno-proteomic tools. Methodology: Clinico-immunological tests were performed to understand the prevalence of sensitivity towards sunflower pollen among the atopic population. Sera from selected sunflower positive patients were used as probe to detect the IgE-reactive proteins from the one and two dimensionally separated proteome of sunflower pollen. The antigenic nature of the sugar moiety of the glycoprotein allergens was studied by meta-periodate modification of IgE-immunoblot. Finally, these allergens were identified by mass-spectrometry (MALDI TOF/TOF and LC ESI qTOF). MASCOT searching was performed against NCBInr database. However, Helianthus annuus genome is not fully sequenced and partially annotated. So in case of low confidence (p> 0.05) protein identification, searching was performed against EST library of Helianthus annuus. Results: Prevalence of sunflower pollen allergy was observed among 21% of the atopic population and associated with elevated level of specific IgE and histamine in the sera of these patients. Immunoscreening of sunflower pollen proteome with patient serum detected seven IgE-reactive proteins with varying molecular weight and pI. Hierarchical clustering of 2D-immunoblot data highlighted three allergens characterized by a more frequent immuno-reactivity and increased levels of IgE antibodies in the sera of susceptible patients. These allergens were considered as the major allergens of sunflower pollen and were found to have their glycan moiety critical for inducing IgE response. Homology driven search of MS/MS data of these IgE-reactive proteins identified seven previously unreported allergens from sunflower pollen. Three major allergenic proteins were identified as two non-isoformic pectate lyases and a cystein protease. Conclusion: Novelty of the present report is the identification of a panel of seven sunflower pollen allergens for the first time at immuno-biochemical and proteomic level, which substantiated the clinical evidence of sunflower allergy. Further purification and recombinant expression of these allergens will improve component-resolved diagnosis and therapy of pollen allergy.
2015-10-05 | PXD002397 | Pride