Combination of transcriptome sequencing and iTRAQ proteome reveals the molecular mechanisms determining petal shape in herbaceous peony (Paeonia lactiflora Pall.)

Multi-Omics Methods Applied to Flower Development

Developmental processes in multicellular organisms depend on the proficiency of cells to orchestrate different gene expression programs. Over the past years, several studies of reproductive organ development have considered genomic analyses of transcription factors and global gene expression changes, modeling complex gene regulatory networks. Nevertheless, the dynamic view of developmental processes requires, as well, the study of the proteome in its expression, complexity, and relationship with the transcriptome. In this chapter, we describe a dual extraction method-for protein and RNA-for the characterization of genome expression at proteome level and its correlation to transcript expression data. We also present a shotgun proteomic procedure (LC-MS/MS) followed by a pipeline for the imputation of missing values in mass spectrometry results.

HpeNet: Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall

The herbaceous peony (Paeonia lactiflora Pall.) is a well-known ornamental flowering and pharmaceutical plant found in China. Its high medicinal value has long been recognized by traditional Chinese medicine (as Radix paeoniae Alba and Radix paeoniae Rubra), and it has become economically valued for its oilseed in recent years; like other Paeonia species, it has been identified as a novel resource for the α-linolenic acid used in seed oil production. However, its genome has not yet been sequenced, and little transcriptome data on Paeonia lactiflora are available. To obtain a comprehensive transcriptome for Paeonia lactiflora, RNAs from 10 tissues of the Paeonia lactiflora Pall. cv Shaoyou17C were used for de novo assembly, and 416,062 unigenes were obtained. Using a homology search, it was found that 236,222 (approximately 57%) unigenes had at least one BLAST hit in one or more public data resources. The construction of co-expression networks is a feasible means for improving unigene annotation. Using in-house transcriptome data, we obtained a co-expression network covering 95.13% of the unigenes. Then we integrated co-expression network analyses and lipid-related pathway genes to study lipid metabolism in Paeonia lactiflora cultivars. Finally, we constructed the online database HpeNet (http://bioinformatics.cau.edu.cn/HpeNet) to integrate transcriptome data, gene information, the co-expression network, and so forth. The database can also be searched for gene details, gene functions, orthologous matches, and other data. Our online database may help the research community identify functional genes and perform research on Paeonia lactiflora more conveniently. We hope that de novo transcriptome assembly, combined with co-expression networks, can provide a feasible means to predict the gene function of species that do not have a reference genome.

Germplasm resources and genetic breeding of Paeonia: a systematic review

Members of the genus Paeonia, which consists of globally renowned ornamentals and traditional medicinal plants with a rich history spanning over 1500 years, are widely distributed throughout the Northern Hemisphere. Since 1900, over 2200 new horticultural Paeonia cultivars have been created by the discovery and breeding of wild species. However, information pertaining to Paeonia breeding is considerably fragmented, with fundamental gaps in knowledge, creating a bottleneck in effective breeding strategies. This review systematically introduces Paeonia germplasm resources, including wild species and cultivars, summarizes the breeding strategy and results of each Paeonia cultivar group, and focuses on recent progress in the isolation and functional characterization of structural and regulatory genes related to important horticultural traits. Perspectives pertaining to the resource protection and utilization, breeding and industrialization of Paeonia in the future are also briefly discussed.

Proteomics analysis reveals the defense priming effect of chitosan oligosaccharides in Arabidopsis-Pst DC3000 interaction

Chitosan oligosaccharides (COS) worked effectively in multiple plant-pathogen interactions as plant immunity regulator, however, due to the complexity of the COS-induced immune signaling network, the topic requires further investigation. In the present study, quantitative analysis of proteins was performed to investigate the underlying mechanism of COS induced resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis thaliana. 4303 proteins were successfully quantified, 186, 217 and 207 proteins were differently regulated in mock + Pst, COS, and COS + Pst treated plants, respectively, compared with mock plants. From detailed functional and hierarchical clustering analysis, a priming effect of COS on plant immune system by pre-regulated the key proteins related to signaling transduction, defense response, cell wall biosynthesis and modification, plant growth and development, gene transcription and translation, which confers enhanced resistance when Pst DC3000 infection in Arabidopsis. Moreover, RACK1B which has the potential to be the key kinase receptor for COS signals was found out by protein-protein interaction network analysis of COS responsive proteins. In conclusion, COS treatment enable plant to fine-tuning its defense mechanisms for a more rapid and stronger response to future pathogen attacks, which obviously enhances plants defensive capacity that makes COS worked effectively in multiple plant-pathogen interactions.

Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony (Paeonia suffruticosa cv. Kao) cultured on media with three browning inhibitors

Tree peony (Paeonia suffruticosa Andrews) has ornamental, oil, and medicinal values, and demand in the markets for uniform tree peony seedlings is increasing. Micropropagation could quickly propagate uniform seedlings. However, the heavy browning phenomenon hinders large-scale development of uniform tree peony seedlings. In this paper, we measured the total phenolic compounds content, and sequenced the transcriptomes of tree peony 'Kao' petiole calluses cultured on media with three browning antagonist treatments and fresh petioles to identify the key genes involved in callus browning. Polyvinylpyrrolidone (PVP) treatment can reduce production of phenolic compounds and promote callus regeneration. A total of 218,957 unigenes were obtained from fresh petiole and three kinds of browning petiole calluses by transcriptome sequencing. The average sequence length of unigenes was 446 bp with an N50 of 493 bp. Functional annotation analysis revealed that 43,428, 45,357, 31,194, 30,019, and 21,357 unigenes were annotated using the NCBI-NR database, Swiss-Prot, KOG, GO, and KEGG, respectively. In total, 33 differentially expressed genes (DEGs) were identified as potentially associated with callus browning. Among these DEGs, 12 genes were predicted to participate in phenolic compounds biosynthesis, three genes were predicted to be involved in phenolic compounds oxidation, and six genes were predicted to participate in callus regeneration. Moreover, six transcription factors were observed to be differentially expressed in the fresh petiole and three treated petioles in tree peony. This study comprehensively identifies browning-related gene resources and will possibly help in deciphering the molecular mechanisms of callus browning of tree peony in the future.

Color characteristics, pigment accumulation and biosynthetic analyses of leaf color variation in herbaceous peony (Paeonia lactiflora Pall.)

Herbaceous peony (Paeonia lactiflora Pall.) is one of the color-leaved ornamental spring plants, with graceful appearance and splendid color. However, the underlying mechanism of this coloration variation from purple to green has not been studied in P. lactiflora. In th study, the leaves in purple, purple-green, and green stages were compared in terms of anatomical, physiological, and molecular. We found that the variation of leaf color from purple to green was mainly determined by the change in pigments distributed in the leaf surface. Physiological experiments showed a significant increase in chlorophyll contents and a notable reduction in anthocyanin contents in leaves from the purple to green stages. We further found that the anthocyanin biosynthesis-related dihydroflavonol 4-reductase (DFR) gene and anthocyanin synthase (ANS) gene as well as chlorophyll biosynthesis-related glutamyl-tRNA reductase (HEMA) gene showed a decreased trend in leaves from purple to green stages, whereas the chlorophyll degradation-related chlorophyll b reductase (NYC) gene showed a rising trend. Alteration of DFR and ANS gene expression might reduce anthocyanin accumulation, whereas increased HEMA gene expression would enhance chlorophyll biosynthesis and reduced NYC gene expression would inhibit chlorophyll degradation. Consequently, reduction in anthocyanins and enhanced deposition of chlorophylls resulted in leaf coloration variation from purple to green in P. lactiflora, which could improve our understanding of its mechanism for further studies.

Advances in molecular biology of Paeonia L

Molecular biology can serve as a tool to solve the limitations of traditional breeding and cultivation techniques related to flower patterns, the improvement of flower color, and the regulation of flowering and stress resistance. These characteristics of molecular biology ensured its significant role in improving the efficiency of breeding and germplasm amelioration of Paeonia. This review describes the advances in molecular biology of Paeonia, including: (1) the application of molecular markers; (2) genomics, transcriptomics, proteomics, metabolomics, and microRNA studies; (3) studies of functional genes; and (4) molecular biology techniques. This review also points out select limitations in current molecular biology, analyzes the direction of Paeonia molecular biology research, and provides advice for future research objectives.