Homeotic transformation from stamen to petal in Eriobotrya japonica is associated with hormone signal transduction and reduction of the transcriptional activity of EjAG

Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L

Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.

Physiology, gene expression, and epiphenotype of two Dianthus broteri polyploid cytotypes under temperature stress

Increasing evidence supports a major role for abiotic stress response in the success of plant polyploids, which usually thrive in harsh environments. However, understanding the ecophysiology of polyploids is challenging due to interactions between genome doubling and natural selection. Here, we investigated physiological responses, gene expression, and the epiphenotype of two related Dianthus broteri cytotypes-with different genome duplications (4× and 12×) and evolutionary trajectories-to short extreme temperature events (42/28 °C and 9/5 °C). The 12× cytotype showed higher expression of stress-responsive genes (SWEET1, PP2C16, AI5L3, and ATHB7) and enhanced gas exchange compared with 4×. Under heat stress, both ploidies had greatly impaired physiological performance and altered gene expression, with reduced cytosine methylation. However, the 12× cytotype exhibited remarkable physiological tolerance (maintaining gas exchange and water status via greater photochemical integrity and probably enhanced water storage) while down-regulating PP2C16 expression. Conversely, 4× D. broteri was susceptible to thermal stress despite prioritizing water conservation, showing signs of non-stomatal photosynthetic limitations and irreversible photochemical damage. This cytotype also presented gene-specific expression patterns under heat, up-regulating ATHB7. These findings provide insights into divergent stress response strategies and physiological resistance resulting from polyploidy, highlighting its widespread influence on plant function.

Genome-Wide Identified MADS-Box Genes in Prunus campanulata 'Plena' and Theirs Roles in Double-Flower Development

The MADS-box gene family plays key roles in flower induction, floral initiation, and floral morphogenesis in flowering plants. To understand their functions in the double-flower formation of Prunus campanulata 'Plena' (hereafter referred to as PCP), which is an excellent flowering cherry cultivar, we performed genome-wide identification of the MADS-box gene family. In this study, 71 MADS-box genes were identified and grouped into the Mα, Mβ, Mγ and MIKC subfamilies according to their structures and phylogenetic relationships. All 71 MADS-box genes were located on eight chromosomes of PCP. Analysis of the cis-acting elements in the promoter region of MADS-box genes indicated that they were associated mainly with auxin, abscisic acid, gibberellin, MeJA (methyl jasmonate), and salicylic acid responsiveness, which may be involved in floral development and differentiation. By observing the floral organ phenotype, we found that the double-flower phenotype of PCP originated from petaloid stamens. The analysis of MIKC-type MADS-box genes in PCP vegetative and floral organs by qRT-PCR revealed six upregulated genes involved in petal development and three downregulated genes participating in stamen identity. Comparative analysis of petaloid stamens and normal stamens also indicated that the expression level of the AG gene (PcMADS40) was significantly reduced. Thus, we speculated that these upregulated and downregulated genes, especially PcMADS40, may lead to petaloid stamen formation and thus double flowers. This study lays a theoretical foundation for MADS-box gene identification and classification and studying the molecular mechanism underlying double flowers in other ornamental plants.

Dynamic Changes of Endogenous Hormones in Different Seasons of Idesia polycarpa Maxim

Idesia polycarpa Maxim is a native dioecious tree from East Asia cultivated for its fruits and as an ornamental plant throughout temperate regions. Given the economic potential, comparative studies on cultivated genotypes are of current interest. This study aims to discover the dynamic changes and potential functions of endogenous hormones in I. polycarpa, as well as the differences in endogenous hormone contents in different growth stages among different I. polycarpa provenances. We used High-Performance Liquid Chromatography (HPLC) to measure and compare the levels of abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin A3 (GA3), and trans-Zeatin-riboside (tZR) in the leaves, flowers, and fruits of I. polycarpa from various provenances between April and October. Our findings indicated that changes in the ABA and GA3 content of plants from Jiyuan and Tokyo were minimal from April to October. However, the levels of these two hormones in Chengdu plants vary greatly at different stages of development. The peak of IAA content in the three plant materials occurred primarily during the early fruit stage and the fruit expansion stage. The concentration of tZR in the three plant materials varies greatly. Furthermore, we discovered that the contents of endogenous hormones in I. polycarpa leaves, flowers, and fruits from Chengdu provenances were slightly higher than those from Tokyo and Jiyuan provenances. The content of IAA was higher in male flowers than in female flowers, and the content of ABA, GA3, and tZR was higher in female flowers than in male flowers. According to the findings, the contents of these four endogenous hormones in I. polycarpa are primarily determined by the genetic characteristics of the trees and are less affected by cultivation conditions. The gender of I. polycarpa had a great influence on these four endogenous hormones. The findings of this study will provide a theoretical foundation and practical guidance for artificially regulating the flowering and fruiting of I. polycarpa.

Transcriptome analysis of critical genes related to flowering in Mikania micrantha at different altitudes provides insights for a potential control

BACKGROUND

Mikania micrantha is a vine with strong invasion ability, and its strong sexual reproduction ability is not only the main factor of harm, but also a serious obstacle to control. M. micrantha spreads mainly through seed production. Therefore, inhibiting the flowering and seed production of M. micrantha is an effective strategy to prevent from continuing to spread.

RESULT

The flowering number of M. micrantha is different at different altitudes. A total of 67.01 Gb of clean data were obtained from nine cDNA libraries, and more than 83.47% of the clean reads were mapped to the reference genome. In total, 5878 and 7686 significantly differentially expressed genes (DEGs) were found in E2 vs. E9 and E13 vs. E9, respectively. Based on the background annotation and gene expression, some candidate genes related to the flowering pathway were initially screened, and their expression levels in the three different altitudes in flower bud differentiation showed the same trend. That is, at an altitude of 1300 m, the flower integration gene and flower meristem gene were downregulated (such as SOC1 and AP1), and the flowering inhibition gene was upregulated (such as FRI and SVP). Additionally, the results showed that there were many DEGs involved in the hormone signal transduction pathway in the flower bud differentiation of M. micrantha at different altitudes.

CONCLUSIONS

Our results provide abundant sequence resources for clarifying the underlying mechanisms of flower bud differentiation and mining the key factors inhibiting the flowering and seed production of M. micrantha to provide technical support for the discovery of an efficient control method.

Genome-wide analysis of the WOX gene family and the role of EjWUSa in regulating flowering in loquat (Eriobotrya japonica)

The WUSCHEL (WUS)-related homeobox (WOX) gene family plays a crucial role in stem cell maintenance, apical meristem formation, embryonic development, and various other developmental processes. However, the identification and function of WOX genes have not been reported in perennial loquat. In this study, 18 EjWOX genes were identified in the loquat genome. Chromosomal localization analysis showed that 18 EjWOX genes were located on 12 of 17 chromosomes. Gene structure analysis showed that all EjWOX genes contain introns, of which 11 EjWOX genes contain untranslated regions. There are 8 pairs of segmental duplication genes and 0 pairs of tandem duplication genes in the loquat WOX family, suggesting that segmental duplications might be the main reason for the expansion of the loquat WOX family. A WOX transcription factor gene named EjWUSa was isolated from loquat. The EjWUSa protein was localized in the nucleus. Protein interactions between EjWUSa with EjWUSa and EjSTM were verified. Compared with wild-type Arabidopsis thaliana, the 35S::EjWUSa transgenic Arabidopsis showed early flowering. Our study provides an important basis for further research on the function of EjWOX genes and facilitates the molecular breeding of loquat early-flowering varieties.

Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloid

BACKGROUND

The cultivated Camellia sasanqua forms a divergent double flower pattern, and the stamen petaloid is a vital factor in the phenomenon. However, the regulation mechanism remains largely unclear.

RESULTS

Here, a comprehensive comparative transcriptome analysis of the wild-type, "semi-double", "peony double", and "rose double" was performed. The cluster analysis of global gene expression level showed petal and stamen difficulty separable in double flower. The crucial pathway and genes related to double flower patterns regulation were identified by pairwise comparisons and weighted gene coexpression network (WGCNA). Divergent genes expression, such as AUX1 and AHP, are involved in plant hormone signaling and photosynthesis, and secondary metabolites play an important role. Notably, the diversity of a petal-specific model exhibits a similar molecular signature to the stamen, containing extensin protein and PSBO1, supporting the stamen petaloid point. Moreover, the expansion of class A gene activity influenced the double flower formation, showing that the key function of gene expression was probably demolished.

CONCLUSIONS

Overall, this work confirmed the ABCE model and provided new insights for elucidating the molecular signature of double formation.

Widely targeted metabolomics reveals stamen petaloid tissue of Paeonia lactiflora Pall. being a potential pharmacological resource

Paeonia lactiflflora Pall. has a long edible and medicinal history because of the very high content of biologically active compounds. However, little information is available about the metabolic basis of pharmacological values of P. lactiflora flowers. In this study, we investigated metabolites in the different parts of P. lactiflora flowers, including petal, stamen petaloid tissue and stamen, by widely targeted metabolomics approach. A total of 1102 metabolites were identified, among which 313 and 410 metabolites showed differential accumulation in comparison groups of petal vs. stamen petaloid tissue and stamen vs. stamen petaloid tissue. Differential accumulated metabolites analysis and KEGG pathway analysis showed that the flavonoids were the most critical differential metabolites. Furthermore, difference accumulation of flavonoids, phenolic acids, tannins and alkaloids might lead to the differences in antioxidant activities and tyrosinase inhibition effects. Indeed, stamen petaloid tissue displayed better antioxidant and anti-melanin production activities than petal and stamen through experimental verification. These results not only expand our understanding of metabolites in P. lactiflora flowers, but also reveal that the stamen petaloid tissues of P. lactiflora hold the great potential as promising ingredients for pharmaceuticals, functional foods and skincare products.

Comparative transcriptome analysis of flower bud transition and functional characterization of EjAGL17 involved in regulating floral initiation in loquat

Floral initiation plays a critical role for reproductive success in plants, especially fruit trees. However, little information is known on the mechanism of the initiation in loquat (Eriobotrya japonica Lindl.). Here, we used transcriptomic, expression and functional analysis to investigate the candidate genes in floral initiation in loquat. Comparative transcriptome analysis showed differentially expressed genes (DEGs) were mainly enriched in the metabolic pathways of plant hormone signal transduction. The DEGs were mainly involved in the gibberellin, auxin, cytokinin, abscisic acid, salicylic acid and ethylene signaling pathways. Meanwhile, some transcription factors, including MADS-box (MCM1, AGAMOUS, DEFICIENS and SRF), MYB (Myeloblastosis), TCP (TEOSINTE BRANCHED 1, CYCLOIDEA and PCF1), WOX (WUSCHEL-related homeobox) and WRKY (WRKY DNA-binding protein), were significantly differentially expressed. Among these key DEGs, we confirmed that an AGL17 ortholog EjAGL17 was significantly upregulated at the flower bud transition stage. Phylogenetic tree analysis revealed that EjAGL17 was grouped into an AGL17 clade of MADS-box transcription factors. Protein sequence alignment showed that EjAGL17 included a distinctive C-terminal domain. Subcellular localization of EjAGL17 was found only in the nucleus. Expression levels of EjAGL17 reached the highest at the development stage of flower bud transition. Moreover, ectopic expression of EjAGL17 in Arabidopsis significantly exhibited early flowering. Our study provides abundant resources of candidate genes for studying the mechanisms underlying the floral initiation in loquat and other Rosaceae species.

Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

In this study, third-generation full-length (FL) transcriptome sequencing was performed of loquat using single-molecule real-time(SMRT) sequencing from the pooled cDNA of embryos of young loquat fruit under different low temperatures (three biological replicates for treatments of 1°C, -1°C, and -3°C, for 12 h or 24 h) and the control group(three biological replicates for treatments of room temperature), Illumina sequencing was used to correct FL transcriptome sequences. A total of 3 PacBio Iso-Seq libraries (1–2 kb, 2–3 kb and 3–6 kb) and 21 Illumina transcriptome libraries were constructed, a total of 13.41 Gb of clean reads were generated, which included 215,636 reads of insert (ROIs) and 121,654 FL, non-chimaric (FLNC) reads. Transcript clustering analysis of the FLNC reads revealed 76,586 consensus isoforms, and a total of 12,520 high-quality transcript sequences corrected with non-FL sequences were used for subsequent analysis. After the redundant reads were removed, 38,435 transcripts were obtained. A total of 27,905 coding DNA sequences (CDSs) were identified, and 407 long non-coding RNAs (lncRNAs) were ultimately predicted. Additionally, 24,832 simple sequence repeats (SSRs) were identified, and a total of 1,295 alternative splicing (AS) events were predicted. Furthermore, 37,993 transcripts were annotated in eight functional databases. This is the first study to perform SMRT sequencing of the FL transcriptome of loquat. The obtained transcriptomic data are conducive for further exploration of the mechanism of loquat freezing injury and thus serve as an important theoretical basis for generating new loquat material and for identifying new ways to improve loquat cold resistance.

An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat

Flower development is a vital developmental process in the life cycle of woody perennials, especially fruit trees. Herein, we used transcriptomic, proteomic, and hormone analyses to investigate the key candidate genes/proteins in loquat (Eriobotrya japonica) at the stages of flower bud differentiation (FBD), floral bud elongation (FBE), and floral anthesis (FA). Comparative transcriptome analysis showed that differentially expressed genes (DEGs) were mainly enriched in metabolic pathways of hormone signal transduction and starch and sucrose metabolism. Importantly, the DEGs of hormone signal transduction were significantly involved in the signaling pathways of auxin, gibberellins (GAs), cytokinin, ethylene, abscisic acid (ABA), jasmonic acid, and salicylic acid. Meanwhile, key floral integrator genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and floral meristem identity genes SQUAMOSA PROMOTER BINDING LIKE (SPL), LEAFY (LFY), APETALA1 (AP1), and AP2 were significantly upregulated at the FBD stage. However, key floral organ identity genes AGAMOUS (AG), AP3, and PISTILLATA (PI) were significantly upregulated at the stages of FBE and FA. Furthermore, transcription factors (TFs) such as bHLH (basic helix-loop-helix), NAC (no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2) and cup-shaped cotyledon (CUC2)), MYB_related (myeloblastosis_related), ERF (ethylene response factor), and C2H2 (cysteine-2/histidine-2) were also significantly differentially expressed. Accordingly, comparative proteomic analysis of differentially accumulated proteins (DAPs) and combined enrichment of DEGs and DAPs showed that starch and sucrose metabolism was also significantly enriched. Concentrations of GA3 and zeatin were high before the FA stage, but ABA concentration remained high at the FA stage. Our results provide abundant sequence resources for clarifying the underlying mechanisms of the flower development in loquat.