Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea

Fan, Zhengqi; Li, Jiyuan; Li, Xinlei; Wu, Bin; Wang, Jiangying; Liu, Zhongchi; Yin, Hengfu

doi:10.1038/srep09729

Cited by 59 publications

(42 citation statements)

References 43 publications

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“…Beside the transcriptomes of tea plant collected from different developmental stages or under different stresses or response to different hormones, we also literately gathered a total of nine transcriptomes from its close relatives, including C. azalea (Fan et al ., ), C. japonica (Li et al ., ), C. meiocarpa (Feng et al ., ), C. nitidissima (Zhou et al ., ), C. oleifera (Xia et al ., ), C. reticulate (Yao et al ., ), C. sasanqua (Huang et al ., ), C. chekiangoleosa (Wang et al ., ) and C. taliensis (Zhang et al ., ). The detail information of each transcriptome that comprises published journal, authors, study background, main conclusion, data accession numbers and investigated tissues was collected.…”

Section: Data Contentmentioning

confidence: 99%

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Xia

Tong

et al. 2019

Plant Biotechnology Journal

236

181

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Summary Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large‐scale omics‐data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web‐accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well‐organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well‐resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

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Section: Data Contentmentioning

confidence: 99%

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Xia

Tong

et al. 2019

Plant Biotechnology Journal

236

181

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“…Clustering pattern analysis of gene expression is commonly used in transcriptome research [34][35][36]. However, we found that some DEGs identified by clustering pattern in this study were differentially expressed in both cultivars of P. rockii, which limited the identification of specific factors.…”

Section: Wgcna Of Carpel Quantitative Variation In P Rockiimentioning

confidence: 60%

“…RNA-seq technology is an important method to obtain effective functional genes in crops, especially for crops without reference genomic information. At present, RNA-seq has been widely used to study floral organ development in woody plants [32][33][34][35][36]. With the development of highthroughput sequencing technology, numerous studies have been carried out by SMLRS or in combination with NGS technology.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

et al. 2019

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Background Quantitative variation of floral organs in plants is caused by an extremely complex process of transcriptional regulation. Despite progress in model plants, the molecular mechanisms of quantitative variation remain unknown in woody flower plants. The Paeonia rockii originated in China is a precious woody plant with ornamental, medicinal and oil properties. There is a wide variation in the number of carpel in P. rockii , but the molecular mechanism of the variation has rarely been studied. Then a comparative transcriptome was performed among two cultivars of P. rockii with different development patterns of carpel in this study. Results Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in P. rockii . Then clustering pattern and weighted gene coexpression network analysis (WGCNA) indicated that 15 candidate genes were likely involved in the carpel quantitative variation, including floral organ development, transcriptional regulatory and enzyme-like factors. Moreover, transcription factors (TFs) from the MYB, WD, RING1 and LRR gene families suggested the important roles in the management of the upstream genes. Among them, PsMYB114-like , PsMYB12 and PsMYB61-like from the MYB gene family were probably the main characters that regulated the carpel quantitative variation. Further, a hypothetical model for the regulation pattern of carpel quantitative variation was proposed in which the candidate genes function synergistically the quantitative variation process. Conclusions We present the high-quality sequencing products in P. rockii . Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. The DEGs are candidate for functional analyses of genes regulating the carpel quantitative variation in tree peonies, which provide a precious resource that reveals the molecular mechanism of carpel quantitative variation in other woody flower crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-6036-z) contains supplementary material, which is available to authorized users.

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“…The characteristic of flowering many times can highlight the ornamental effects of woody plants. Flower bud differentiation was generally considered to be a symbol of flowering in recent studies on plant flowering regulation, such as Arabidopsis thaliana, Camellia azalea [33], and Carya cathayensis [6]. During the annual growth and development of 'Changchun', some flower buds formed by reproductive transformation begin to flower in summer, while the remaining flower buds grow slowly.…”

Section: Flowering Initiation Is An Important Stage During 'Changchunmentioning

confidence: 99%

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

Jiang

Sun

Wei

et al. 2019

Genes

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Magnolia × soulangeana 'Changchun' are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in 'Changchun'. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in 'Changchun'. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up-and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.Genes 2020, 11, 15 2 of 18 Using Solexa/Illumina sequencing platform, researchers have identified almost all transcripts involved in flowering from the vegetative and flower buds in Dimocarpus longan, including putative homologues of DELLA protein, LFY (LEAFY), SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO1) [2]. Meanwhile, compared to the apical meristem of vegetative growth, gibberellin 3 beta-hydroxylase 2 and LFY were both expressed higher in early flowering, indicated that GA pathway may be related to the early flowering of Angelica sinensis [3]. By comparing the differences in transcript expression levels between flowering and non-flowering Moso bamboo samples at different flowering developmental stages, researchers found that GAMYB, GID1 (GIBBERELLIN INSENSITIVE DWARF1), and GID2 were significantly up-regulated, while DELLA protein was down-regulated, and believed that bamboo flowering was associated with gibbere...

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Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea

Cited by 59 publications

References 43 publications

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

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

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