Transcriptome profiling for floral development in reblooming cultivar ‘High Noon’ of Paeonia suffruticosa

Abstract

Tree peony (Paeonia suffruticosa Andrew) is a popular ornamental plant due to its large, fragrant and colorful flowers. The floral development is the most important event in its lifecycle. To explore the mechanism that regulate flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea, using both full-length isoform-sequencing (ISO-seq) and RNA-seq were sequenced. A total of 15.94 Gb raw data were generated in full-length transcriptome sequencing of the 3 floral developmental stages, resulting 0.11 M protein-coding transcripts. Over 457.0 million reads were obtained by RNA-seq in the 3 floral buds. Here, we openly released the full-length transcriptome database of ‘High Noon’ and RNA-seq database of floral development. These databases can provide a fundamental genetic information of tree peony to investigate its transcript structure, variants and evolution. Data will facilitate to deep analyses of the transcriptome for flower development.

Transcriptome analysis of floral bud development and function analysis of a novel CO gene in Paeonia × lemoinei ‘High Noon’

“…To uncover the underlying mechanism of the floral bud formation, the transcriptome dynamics of the three stages were analyzed using the transcriptome data containing a reference isoform transcriptome sequencing data and an expression profile of the floral meristem development described in the previous study 29 . A total of 5816 DEGs were identified with a fold change threshold ≥ 2 and q- value ≤ 0.001 and ten genes were selected to verify the reliability of RNA-seq data (Table S1 , Fig.…”

“…An equal amount of mRNA from floral buds in VS, DS and DCS was mixed and conducted to the ISO-seq, and three independent biological replicates in VS, DS and DCS were subjected in the RNA-seq. The sequencing method was described in detail in our previous study 29 . The referencing ISO-seq data and RNA-seq data were downloaded from the NCBI Sequence Read Archive (SRA) database (SRP212254) and Gene Expression Omnibus (GEO) (GSE133476).…”

“…In previous studies, the unigenes were assembled de novo from the transcriptome of different cultivars, ignoring the variants between cultivars, and the DEGs were screened from buds at only one stage, which cannot represent the true expression pattern of genes during floral transition and floral development 27 , 28 . In consideration of the temporal and spatial pattern of gene expression, three stages in floral bud development were sequenced using full-length isoform sequencing and RNA-seq to generate a reference transcriptome and gene expression profile in our previous study 29 , though deep analysis was not done in the previous study. In this study, the regulation pathways underlying the floral bud development in tree peony were revealed, and candidate genes were screened out based on these data.…”

Integrative Analyses of Transcriptomes and Metabolomes Reveal Associated Genes and Metabolites with Flowering Regulation in Common Vetch (Vicia sativa L.)

“…RNA-Seq is an efficient and powerful tool for profiling the complete gene space of any organism, and it is used to study the flowering regulation mechanism in many plants, such as M. sativa , Gossypium hirsutum , Paeonia suffruticosa , and Hemerocallis citrina [ 1 , 30 , 47 , 48 ]. Metabolomics is the characterization of the metabolites that are present in an organism based on gas chromatography–mass spectrometry (GC-MS), liquid chromatography–mass spectrometry (LC-MS), and nuclear magnetic resonance platforms, and it is divided into four categories: the target analysis of metabolites, metabolic profiling, metabolomics, and metabolic fingerprint analysis [ 49 ].…”

PacBio full-length sequencing integrated with RNA-seq reveals the molecular mechanism of waterlogging and its recovery in Paeonia ostii

“…As a next-generation sequencing (NGS) technique, RNA-sequencing has become an indispensable tool for transcriptome-wide analysis of differential gene expression and gene regulatory networks ( Hu et al., 2020 ). RNA-seq provides a precise and comprehensive analysis of RNA transcripts that affect gene expression ( Chang et al., 2019 ). It has recently been widely used for researching P. ostii gene expression in response to various stresses, including chill-induced stress ( Gai et al., 2013 ), copper stress ( Wang et al., 2016 ), and drought-induced stress ( Zhao et al., 2019 ).…”