Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species
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SUBMITTER: Wu X
PROVIDER: S-EPMC10570465 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:Quantitative real-time PCR (qPCR) is a popular and powerful tool used to understand the molecular mechanisms of flower development. However, the accuracy of this approach depends on the stability of reference genes. The capitulum of chrysanthemums is very special, which is consisting of ray florets and disc florets. There are obvious differences between the two types of florets in symmetry, gender, histological structure, and function. Furthermore, the ray florets have various shapes. The objective of present study was to identify the stable reference genes in Chrysanthemum morifolium and Chrysanthemum lavandulifolium during the process of flower development. In this study, nine candidate reference genes were selected and evaluated for their expression stability acrosssamples during the process of flower development, and their stability was validated by four different algorithms (Bestkeeper, NormFinder, GeNorm, and Ref-finder). SAND (SAND family protein) was found to be the most stably expressed gene in all samples or different tissues during the process of C. lavandulifolium development. Both SAND and PGK (phosphoglycerate kinase) performed most stable in Chinese large-flowered chrysanthemum cultivars, and PGK was the best in potted chrysanthemums. There were differences in best reference genes among varieties as the genetic background of them were complex. These studies provide guidance for selecting reference genes for analyzing the expression pattern of floral development genes in chrysanthemums.
| S-EPMC4786574 | biostudies-literature
Project description:BackgroundRWP-RKs are plant specific transcription factors, which are widely distributed in plants in the form of polygenic families and play key role in nitrogen absorption and utilization, and are crucial to plant growth and development. However, the genome-wide identification and function of RWP-RK in Compositae plants are widely unknown.ResultsIn this study, 101 RWP-RKs in Chrysanthemum lavandulifolium were identified and tandem repeat was an important way for the expansion of RWP-RKs in Compositae species. 101 RWP-RKs contain 38 NIN-like proteins (NLPs) and 31 RWP- RK domain proteins (RKDs), as well as 32 specific expansion members. qRT-PCR results showed that 7 ClNLPs in leaves were up-regulated at the floral transition stage, 10 ClNLPs were negatively regulated by low nitrate conditions, and 3 of them were up-regulated by optimal nitrate conditions. In addition, the flowering time of Chrysanthemum lavandulifolium was advanced under optimal nitrate conditions, the expression level of Cryptochromes (ClCRYs), phytochrome C (ClPHYC) and the floral integration genes GIGANTEA (ClGI), CONSTANS-LIKE (ClCOL1, ClCOL4, ClCOL5), FLOWERING LOCUS T (ClFT), FLOWERING LOCUS C (ClFLC), SUPPRESSOR OF OVER-EXPRESSION OF CONSTANS 1 (ClSOC1) also were up-regulated. The expression level of ClCRY1a, ClCRY1c, ClCRY2a and ClCRY2c in the vegetative growth stage induced by optimal nitrate reached the expression level induced by short-day in the reproductive growth stage, which supplemented the induction effect of short-day on the transcription level of floral-related genes in advance.ConclusionsIt was speculated that ClNLPs may act on the photoperiodic pathway under optimal nitrate environment, and ultimately regulate the flowering time by up-regulating the transcription level of ClCRYs. These results provide new perspective for exploring the mechanism of nitrate/nitrogen affecting flowering in higher plants.
| S-EPMC10105424 | biostudies-literature
Project description:Chrysanthemum lavandulifolium Raw sequence reads
| PRJNA956687 | ENA
Project description:Chrysanthemum lavandulifolium Raw sequence reads
| PRJNA956717 | ENA
Project description:Chrysanthemum lavandulifolium overview
| PRJNA812304 | ENA
Project description:Chrysanthemum ×morifolium is well known throughout the world for its diverse and exquisite flower types. However, due to the complicated genetic background of C. ×morifolium, it is difficult to understand the molecular mechanism of its flower development. And it limits the molecular breeding of improving chrysanthemum flower types. C. ×morifolium has the typical radial capitulum, and many researches showed that the members of the MIKCc-type MADS box gene family play a key role in the formation and development of the capitulum. However, it has been difficult to isolate the important MIKCc and investigate their roles in this process due to the lack of genomic information in chrysanthemum. Here, we identified MIKCc-type MADS box genes at whole genome-wide level in C. lavandulifolium, a diploid species closely related to C. ×morifolium, and investigated their roles in capitulum development by gene expression pattern analysis and protein interaction analysis. A total of 40 ClMIKCc were identified and were phylogenetically grouped into 12 clades. Members of all clades showed different enriched expression patterns during capitulum formation. We speculate that the E-class genes in C. lavandulifolium underwent subfunctionalization because they have a significantly expanded, more diverse expression patterns, and specifically tissue expression than AtSEPs. Meanwhile, we detected the C-class expressed in disc floret corolla, which could be the clue to explore the morphological differences between disc and ray floret corolla. In addition, the potential roles of some MIKCcs in complex inflorescence formation were explored by comparing the number and phylogenetic relationship of MIKCc subfamily members in Asteraceae with different capitulum types. Members of the FLC branch in Asteraceae were found to be possibly related to the differentiation and development of the ray floret.
| S-EPMC10076714 | biostudies-literature
Project description:The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene ClNUM1 cloned from C. lavandulifolium. The results showed that ClNUM1.1 and ClNUM1.2 had selective 3' splicing and selective 5' splicing, and ClNUM1.3 had selective 5' splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the ClNUM1.1 gene and the ClNUM1.2 gene enhanced salt and low-temperature tolerance and the ClNUM1.3 gene enhanced low-temperature tolerance; in mature tobacco plants, the ClNUM1.1 gene was able to enhance salt and low-temperature tolerance, and the ClNUM1.2 and ClNUM1.3 genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the ClNUM1 gene provided new potential genes and research directions for abiotic resistance breeding in Chrysanthemum.
| S-EPMC11201747 | biostudies-literature
Project description:The chrysanthemum is widely used as a cut flower, potted flower, and garden flower worldwide and has high ornamental, edible, and medicinal value. The flower heads, composed of ray florets and disc florets, are the most diverse in terms of morphology among ornamental plants. Here, we compared and analyzed the developmental processes of different capitulum types as well as ray florets and disc florets. Morphological differentiation of the two florets occurred on the dorsal domain of the petals at stage Ⅳ of flower development, and differences in stamen development occurred at stage Ⅴ. The dorsal domain of the ray florets and the early stage of flower development were also an essential site and period, respectively, for the differences among capitulum types. In situ hybridization revealed that CmCYC2c, whose homologs are involved in the specification of floret identity in Asteraceae, was expressed in both the dorsal and ventral domains of the ray petals in the tubular-type chrysanthemum, whereas, it was differentially transcribed in the ray petals of flat- and spoon-type chrysanthemum cultivars and had lower or no expression in the dorsal domain and higher expression in the ventral domain at stage Ⅳ. Our study indicates that the expression pattern of CmCYC2c on the dorsal domain of the ray floret at stage Ⅳ contributes to the formation of diverse flower head types in chrysanthemums.
| S-EPMC10647454 | biostudies-literature
Project description:TCP transcription factors are a unique class of transcription factors that play important roles in alleviating abiotic stresses such as drought and salt. In this study, the whole-genome data of three cultivated varieties, namely, "SFS", "Sang" and "OT3098v2", were utilized to identify and analyze the members of the TCP gene family in oats, and their responses to two abiotic stresses, drought and salt, were also investigated. Results showed that there are 83, 65, and 30 non-redundant TCP genes in the three oats, with the highest number of TCP genes specific to the "SFS", reaching 22 genes. The oat TCP genes can be classified into three subfamilies: PCF, CIN, and CYC/TB1. Most AsTCP genes have important motifs, Motif 1 and Motif 2, which are part of the bHLH domain. Additionally, various cis-acting elements related to hormone response, abiotic stress, light response, and growth and development were found in the promoters of AsTCP genes. The main amplification mechanism of the oat TCP gene family is fragment duplication. Two tandem duplications, AsTCP058/AsTCP059 and AsTCP023/AsTCP025, are stably present in the three oats. The highest number of AsTCP collinear relationships exist in the "SFS" with 89 pairs. After drought and salt stress treatments, significant differences in gene expression were observed among different oat cultivars and treatment periods. Genes that showed significant expression changes under both treatments (AsTCP021, AsTCP033, AsTCP044, AsTCP053, and AsTCP058) may play important roles in oat's response to abiotic stresses. Notably, AsTCP053 gene was significantly upregulated at 24 h of stress treatment and showed a more sensitive response to salt stress. This study provides insights into the functional characterization of the oat TCP gene family and its molecular mechanisms underlying stress tolerance.
| S-EPMC11832536 | biostudies-literature
Project description:Cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but the molecular mechanism of capitulum development remains unclear. Here, we report a 2.60 Gb chromosome-scale reference genome of C. lavandulifolium, a wild Chrysanthemum species found in China, Korea and Japan. The evolutionary analysis of the genome revealed that only recent tandem duplications occurred in the C. lavandulifolium genome after the shared whole genome triplication (WGT) in Asteraceae. Based on the transcriptomic profiling of six important developmental stages of the radiate capitulum in C. lavandulifolium, we found genes in the MADS-box, TCP, NAC and LOB gene families that were involved in disc and ray floret primordia differentiation. Notably, NAM and LOB30 homologs were specifically expressed in the radiate capitulum, suggesting their pivotal roles in the genetic network of disc and ray floret primordia differentiation in chrysanthemum. The present study not only provides a high-quality reference genome of chrysanthemum but also provides insight into the molecular mechanism underlying the diverse capitulum types in chrysanthemum.
| S-EPMC8771455 | biostudies-literature