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Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum.

ABSTRACT: Chrysanthemum is a leading cut flower species. Most conventional cultivars flower during the fall, but the Chrysanthemum morifolium 'Yuuka' flowers during the summer, thereby filling a gap in the market. To date, investigations of flowering time determination have largely focused on fall-flowering types. Little is known about molecular basis of flowering time in the summer-flowering chrysanthemum. Here, the genome-wide transcriptome of 'Yuuka' was acquired using RNA-Seq technology, with a view to shedding light on the molecular basis of the shift to reproductive growth as induced by variation in the photoperiod.Two sequencing libraries were prepared from the apical meristem and leaves of plants exposed to short days, three from plants exposed to long days and one from plants sampled before any photoperiod treatment was imposed. From the ~316 million clean reads obtained, 115,300 Unigenes were assembled. In total 70,860 annotated sequences were identified by reference to various databases. A number of transcription factors and genes involved in flowering pathways were found to be differentially transcribed. Under short days, genes acting in the photoperiod and gibberellin pathways might accelerate flowering, while under long days, the trehalose-6-phosphate and sugar signaling pathways might be promoted, while the phytochrome B pathway might block flowering. The differential transcription of eight of the differentially transcribed genes was successfully validated using quantitative real time PCR.A transcriptome analysis of the summer-flowering cultivar 'Yuuka' has been described, along with a global analysis of floral transition under various daylengths. The large number of differentially transcribed genes identified confirmed the complexity of the regulatory machinery underlying floral transition.

SUBMITTER: Ren L

PROVIDER: S-EPMC4995656 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum.

Ren Liping L Liu Tao T Cheng Yue Y Sun Jing J Gao Jiaojiao J Dong Bin B Chen Sumei S Chen Fadi F Jiang Jiafu J

BMC genomics 20160824

<h4>Background</h4>Chrysanthemum is a leading cut flower species. Most conventional cultivars flower during the fall, but the Chrysanthemum morifolium 'Yuuka' flowers during the summer, thereby filling a gap in the market. To date, investigations of flowering time determination have largely focused on fall-flowering types. Little is known about molecular basis of flowering time in the summer-flowering chrysanthemum. Here, the genome-wide transcriptome of 'Yuuka' was acquired using RNA-Seq techno ...[more]

PMID: 27552984

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Project description:BackgroundChrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular mechanisms of flower development in chrysanthemum.ResultsThe transcriptomes of chrysanthemum vegetative buds, floral buds and buds were sequenced using Illumina paired-end sequencing technology. A total of 15.4 Gb of reads were assembled into 91,367 unigenes with an average length of 739 bp. A total of 43,137 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 25,424, 24,321 and 13,704 unigenes were assigned to 56 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1,876 differentially expressed genes (DEGs) (1,516 up-regulated, 360 down-regulated) were identified between vegetative buds and floral buds, and 3,300 DEGs (1,277 up-regulated, 1,706 down-regulated) were identified between floral buds and buds. Many genes encoding important transcription factors (e.g., AP2, MYB, MYC, WRKY, NAC and CRT) as well as proteins involved in carbohydrate metabolism, protein kinase activity, plant hormone signal transduction, and the defense responses, among others, were considerably up-regulated in floral buds. Genes involved in the photoperiod pathway and flower organ determination were also identified. These genes represent important candidate genes for molecular cloning and functional analysis to study flowering regulation in chrysanthemum.ConclusionThis comparative transcriptome analysis revealed significant differences in gene expression and signaling pathway components between the vegetative buds, floral buds and buds of Chrysanthemum morifolium. A wide range of genes was implicated in regulating the phase transition from vegetative to reproductive growth. These results should aid researchers in the study of flower-time regulation, breeding and molecular biology in chrysanthemum.

Project description:BackgroundChrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils.ResultsWe conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding.ConclusionsThe whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.

Project description:BackgroundChrysanthemum morifolium is one of the most important global cut flower and pot plants, and has been cultivated worldwide. However, limited genomic resources are available and the molecular mechanisms involved in the two morphologically distinct floret developmental cycles in chrysanthemum remain unclear.ResultsThe transcriptomes of chrysanthemum ray florets, disc florets and leaves were sequenced using Illumina paired-end sequencing technology. In total, 16.9 G reads were assembled into 93,138 unigenes with an average length of 738 bp, of which 44,364 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 26,320, 22,304 and 13,949 unigenes were assigned to 54 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1863 differentially expressed genes (DEGs) (1210 up-regulated and 653 down-regulated) were identified between ray florets and disc florets, including genes encoding transcription factors and protein kinases. GO and KEGG pathway enrichment analyses were performed on the DEGs to identify differences in the biological processes and pathways between ray florets and disc florets. The important regulatory genes controlling flower development and flower organ determination, as well as important functional genes in the anthocyanin biosynthetic pathway, were identified, of which two leucoanthocyanidin dioxygenase-encoding genes showed specific expression in ray florets. Lastly, reverse transcription quantitative PCR was conducted to validate the DEGs identified in our study.ConclusionsComparative transcriptome analysis revealed significant differences in patterns of gene expression and signaling pathways between ray florets and disc florets in Chrysanthemum morifolium. This study provided the first step to understanding the molecular mechanism of the differential development of ray florets and disc florets in chrysanthemum, and also provided valuable genomic resources for candidate genes applicable for the breeding of novel varieties in chrysanthemum.

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Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum.

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Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum.

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