De novo sequencing of tree peony (Paeonia suffruticosa) transcriptome to identify critical genes involved in flowering and floral organ development

Abstract

Background Tree peony ( Paeonia suffruticosa Andrews) is a globally famous ornamental flower, with large and colorful flowers and abundant flower types. However, a relatively short and uniform flowering period hinders the applications and production of ornamental tree peony. Unfortunately, the molecular mechanism of regulating flowering time and floral organ development in tree peony has yet to be elucidated. Because of the absence of genomic information, 454-based transcriptome sequence technology for de novo transcriptomics was used to identify the critical flowering genes using re-blooming, non-re-blooming, and wild species of tree peonies. Results A total of 29,275 unigenes were obtained from the bud transcriptome, with an N50 of 776 bp. The average length of unigenes was 677.18 bp, and the longest sequence was 5815 bp. Functional annotation showed that 22,823, 17,321, 13,312, 20,041, and 9940 unigenes were annotated by NCBI-NR, Swiss-Prot, COG, GO, and KEGG, respectively. Within the differentially expressed genes (DEGs) 64 flowering-related genes were identified and some important flowering genes were also characterized by bioinformatics methods, reverse transcript polymerase chain reaction (RT-PCR), and rapid-amplification of cDNA ends (RACE). Then, the putative genetic network of flowering induction pathways and a floral organ development model were put forward, according to the comparisons of DEGs in any two samples and expression levels of the important flowering genes in differentiated buds, buds from different developmental stages, and with GA or vernalization treated. In tree peony, five pathways (long day, vernalization, autonomous, age, and gibberellin) regulated flowering, and the floral organ development followed an ABCE model. Moreover, it was also found that the genes PsAP1 , PsCOL1 , PsCRY1 , PsCRY2 , PsFT , PsLFY , PsLHY , PsGI , PsSOC1 , and PsVIN3 probably regulated re-blooming of tree peony. Conclusion This study provides a comprehensive report on the flowering-related genes in tree peony for the first time and investigated the expression levels of the critical flowering related genes in buds of different cultivars, developmental stages, differentiated primordium, and flower parts. These results could provide valuable insights into the molecular mechanisms of flowering time regulation and floral organ development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5857-0) contains supplementary material, which is available to authorized users.

Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies

“…In this study, N50 was 1,780 bp, indicating a good assembly. The average length of measured sequence obtained was 1,189 bp, which was higher than that of other tree peony researches [8,17], Syringa oblata (853 bp) [23], flowering Chinese cabbage (779 bp) [24], and bamboo (736 bp) [25]. After assembly, a total of 86,195 unigenes were obtained, among which 49, 172 were annotated into the NR database.…”

“…A total of 29,275 unigenes were obtained from the bud transcriptome of tree peony. Among the DEGs, 64 flowering-related genes, and the genes of PsAP1, PsCOL1, PsCRY1, PsCRY2, PsFT, PsLFY, PsLHY, PsGI, PsSOC1, and PsVIN3 probably regulated reblooming [8]. A large number of DEGs on the transcriptome data of tree peony (P. ostii) seeds were related to oil biosynthesis and fatty acid metabolism [9].…”

Flowering in Persian walnut: patterns of gene expression during flower development

“…Certainly, studying the complete genome is necessary to gain a comprehensive understanding of the gene network involved in flowering. Utilizing powerful genetic tools based on next generation sequencing are an effective strategy for studying complex gene networks in flowering [19,20].…”

“…Currently, researchers are widely using transcriptomics and other powerful genetic tools based on next generation sequencing to study complex gene networks involved in flowering. These studies provide a comprehensive understanding of the gene network involved in flowering of model and nonmodel plants [19,20].…”

A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana ‘Changchun’

“…Moreover, Roche/454 sequencing was used to understand the pistillate flowering in Carya cathayensis, which found that the flowering event of pistillate flower buds in hickory was triggered by several pathways synchronously, including GA pathway [6]. Using reblooming, non-re-blooming, and wild-type tree peonies (Paeonia suffruticosa), Wang et al pointed that PsGID1 was important GA signaling genes, and suggested that GA pathway played an important role in the flowering regulation of tree peony [7]. Similar research results were also found in Populus L. [8], Prunus mume [9], Poncirus trifoliata [10] and other woody plants.…”