Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (Rosa chinensis).

The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development.

iTRAQ-based quantitative proteomic analysis reveals dynamic changes during daylily flower senescence.

MAIN CONCLUSION: Sugar-related metabolic biological processes and metabolic pathways as well as invertase, protease, and ribosomal proteins may be critical regulators controlling the circadian rhythm and ephemeral properties of daylily flowers. Daylily is a familiar perennial flower. The daylily flower opens at dawn and withers away at night. Flower longevity in almost all daylily varieties from opening to fading is less than 24 h. In the past decades, the physiological changes and genetic responses to senescence in daylily flowers have been reported. However, the main metabolic pathways and biological processes involved in daylily flower senescence and the proteins involved in premature senility of daylily flowers are poorly understood. Herein, we identified differences between the proteomes of four developmental stages (s1-s4) of daylily flowers using iTRAQ-based quantitative proteomic methods. A total of 445 proteins (containing at least two unique peptides) were identified, and differentially expressed proteins (upregulation ≥ 1.5 or downregulation ≤ 0.67, P value ≤ 0.05) were detected between these stages in the following numbers: 58 (s2/s1), 59 (s3/s1), 31 (s3/s2), 64 (s4/s1), 52 (s4/s2), and 29 (s4/s3). Protein functions and classifications were analyzed based on GO, KEGG, and COG, and expressive hierarchical cluster analysis and functional enrichment analysis for differentially expressed proteins were carried out. A comparison of the late stages (s3 and s4) with the early stage (s1) revealed that the sugar (hexose, monosaccharide, and glucose) metabolic process GO category was the most enriched, and sugar (galactose, pentose, starch, and sucrose) metabolism pathways constituted the most enriched KEGG category. Finally, the potential research value of invertase, protease, and ribosomal proteins for revealing the mechanism underlying the circadian rhythm and ephemeral properties of daylily flowers are discussed. These data and analyses provide new insight into the senescence mechanism of daylily flowers.

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae).

Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species' chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.

The Chromosome-Scale Assembly of the Curcuma alismatifolia Genome Provides Insight Into Anthocyanin and Terpenoid Biosynthesis.

Curcuma alismatifolia, a bulbous flower known for its showy bracts, is widely used around the world as a cut flower, potted, and garden plant. Besides its ornamental value, this species is rich in terpenoid metabolites and could serve as a resource for essential oils. Here, we report a chromosome-level genome assembly of C. alismatifolia and describe its biosynthetic pathways for anthocyanins and terpenoids. This high-quality, assembled genome size is 991.3 Mb with a scaffold N50 value of 56.7 Mb. Evolutionary analysis of the genome suggests that C. alismatifolia diverged from Zingiber officinale about 9.7 million years ago, after it underwent a whole-genome duplication. Transcriptome analysis was performed on bracts at five developmental stages. Nine highly expressed genes were identified, encoding for six enzymes downstream of the anthocyanin biosynthetic pathway. Of these, one gene encoding F3'5'H might be a key node in the regulation of bract color formation. Co-expression network analysis showed that MYB, bHLH, NAC, and ERF transcription factors collectively regulated color formation in the bracts. Characterization of terpenoid biosynthesis genes revealed their dispersal and tandem duplications, both of which contributed greatly to the increase in the number of terpene synthase genes in C. alismatifolia, especially to species-specific expansion of sesquiterpene synthase genes. This work facilitates understanding of genetic basis of anthocyanin and terpenoid biosynthesis and could accelerate the selective breeding of C. alismatifolia varieties with higher ornamental and medicinal value.

Ectopic expression of the AaFUL1 gene identified in Anthurium andraeanum affected floral organ development and seed fertility in tobacco.

Anthurium andraeanum is a high-grade potted flower that enjoys global popularity. Its floral organs have been substantially modified, and its ornamental value is based on its petaloid bracts. MADS-box gene products are important transcription factors that control plant development. In particular, the APETALA1 (AP1)/FRUITFULL (FUL) family of MADS-box genes plays a key role in flowering transitions and out-whorl floral organ identity specification. In this report, one FUL-like gene was cloned from Anthurium andraeanum and named AaFUL1 after bioinformatics identification. Subsequent subcellular localization experiments confirmed that the AaFUL1 protein was located in the nucleus, and data obtained from an expression analysis indicated that the relative expression level of AaFUL1 was the highest in bracts and inflorescences, while its expression was relatively low in stems and roots. Next, an AaFUL1 overexpression vector was constructed and ectopically expressed in tobacco. The transformants did not show any early flowering phenotype, but the average internode length of the inflorescence branch was significantly higher than that observed in the control, and its petal color had substantially faded. The morphology of the petal and pistil was clearly changed, the fruit was deformed, and the seed was largely aborted. These data indicate that even though the sequence of AaFUL1 is relatively conserved, its function differs from that of other orthologs, and the FUL subfamily of MADS-box transcription factors may have taken on new functions during the evolution processes. The results of this experiment enrich our knowledge of FUL transcription factors in monocotyledon plants.

Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa.

Dehydration-responsive element-binding factor 2 (DREB2) belongs to the C-repeat-binding factor (CBF)/DREB subfamily of proteins. In this study, a 2,245 bp PsDREB2 promoter fragment was isolated from the genome of Paeonia suffruticosa. The fragment was rich in A/T bases and contained TATA box sequences, abscisic acid (ABA)-response elements, and other cis-elements, such as MYB and CAAT box. The promoter was fused with the ß-glucuronidase (GUS) reporter gene to generate an expression vector. Arabidopsis thaliana was transformed with a flower dipping method. Gus activity in different tissues and organs of transgenic plants was determined via histochemical staining and quantified via GUS fluorescence. The activity of promoter regulatory elements in transgenic plants under drought, low-temperature, high-salt, and ABA stresses was analyzed. The results showed that the PsDREB2 gene promoter was expressed in the roots, stems, leaves, flowers, and silique pods but not in the seeds of transgenic Arabidopsis. Furthermore, the promoter was induced by drought, low temperature, high salt, and ABA. Hence, the PsDREB2 promoter is tissue- and stress-specific and can be used in the genetic engineering of novel peony cultivars in the future.

Piriformospora indica-induced phytohormone changes and root colonization strategies are highly host-specific.

Piriformospora indica, an endophytic fungus of Sebacinales, has a wide host range and promotes the performance of mono- and eudicot plants. Here, we compare the interaction of P. indica with the roots of seven host plants (Anthurium andraeanum, Arabidopsis thaliana, Brassica campestris, Lycopersicon esculentum, Oncidium orchid, Oryza sativa, and Zea mays). Microscopical analyses showed that the colonization time and the mode of hyphal invasion into the roots differ in the symbiotic interactions. Substantial differences between the species were also observed for the levels and accumulation of jasmonate (JA) and gibberellin (GA) and the transcript levels for genes involved in their syntheses. No obvious correlation could be detected between the endogenous JA and/or GA levels and the time point of root colonization in a given plant species. Our results suggest that root colonization strategies and changes in the two phytohormone levels are highly host-specific.

Cloning and functional analysis of a novel ascorbate peroxidase (APX) gene from Anthurium andraeanum.

An 888-bp full-length ascorbate peroxidase (APX) complementary DNA (cDNA) gene was cloned from Anthurium andraeanum, and designated as AnAPX. It contains a 110-bp 5'-noncoding region, a 28-bp 3'-noncoding region, and a 750-bp open reading frame (ORF). This protein is hydrophilic with an aliphatic index of 81.64 and its structure consisting of α-helixes, ß-turns, and random coils. The AnAPX protein showed 93%, 87%, 87%, 87%, and 86% similarities to the APX homologs from Zantedeschia aethiopica, Vitis pseudoreticulata, Gossypium hirsutum, Elaeis guineensis, and Zea mays, respectively. AnAPX gene transcript was measured non-significantly in roots, stems, leaves, spathes, and spadices by real-time polymerase chain reaction (RT-PCR) analysis. Interestingly, this gene expression was remarkably up-regulated in response to a cold stress under 6 °C, implying that AnAPX might play an important role in A. andraeanum tolerance to cold stress. To confirm this function we overexpressed AnAPX in tobacco plants by transformation with an AnAPX expression construct driven by CaMV 35S promoter. The transformed tobacco seedlings under 4 °C showed less electrolyte leakage (EL) and malondialdehyde (MDA) content than the control. The content of MDA was correlated with chilling tolerance in these transgenic plants. These results show that AnAPX can prevent the chilling challenged plant from cell membrane damage and ultimately enhance the plant cold tolerance.

Agrobacterium tumefaciens-mediated transformation of Narcissus tazzeta var. chinensis.

Phytoene synthase (PSY), as a key regulatory enzyme for carotene biosynthesis, plays an important role in regulating color formation in many species. In the present study, a protocol was developed for the transformation of Narcissus tazzeta var chinensis using Agrobacterium tumefaciens strain LBA4404 harboring a binary vector pCAMBIA1301 plasmid which contained an antisense phytoene synthase gene, a reporter beta-glucuronidase gene and a selectable marker hygromycin phosphotransferase gene. Effects of some factors on efficiency of transformation and regeneration were examined. Preculture of the explants for 6 days before inoculation enhanced the transient GUS expression. The addition of acetosyringone (AS) at 100 micromol l(-1) for inoculation and a period of 3 days co-cultivation yielded efficient transient GUS expression. Transformants were obtained through selection on MS medium containing 5 mg l(-1) 6-benzylaminopurine (BA), 0.1 mg l(-1)alpha-naphthalene acetic acid (NAA) and 40 mg l(-1) hygromycin. The transformation frequency was 1.24% based on PCR analysis of gus gene. One or two copies of transgene were demonstrated in different transformations by Southern blotting analyses. Northern blotting results confirmed that the transcription of the endogenous psy gene in transgenic plants was inhibited or silenced. The method reported here provides new opportunities for improvement of quality traits of Narcissus tazzeta via genetic transformation.