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de novo transcriptome flowering

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https://www.readbyqxmd.com/read/28992542/de-novo-transcriptome-sequencing-of-camellia-sasanqua-and-the-analysis-of-major-candidate-genes-related-to-floral-traits
#1
Hui Huang, En-Hua Xia, Hai-Bin Zhang, Qiu-Yang Yao, Li-Zhi Gao
Camellia sasanqua is one of the most famous horticultural plants in Camellia (Theaceae) due to its aesthetic appeal as landscape plant. Knowledge regarding the genetic basis of flowering time, floral aroma and color in C. sasanqua is limited, but is essential to breed new varieties with desired floral traits. Here, we described the de novo transcriptome of young leaves, flower buds and flowers of C. sasanqua. A total of 60,127 unigenes were functionally annotated based on the sequence similarity. After analysis, we found that two floral integrator genes, SOC1 and AP1, in flowering time pathway showed evidence of gene family expansion...
September 1, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28981620/dissecting-the-bacon-and-eggs-phenotype-transcriptomics-of-post-anthesis-colour-change-in-lotus
#2
Mannfred M A Boehm, Dario I Ojeda, Quentin C B Cronk
Background and Aims: Post-anthesis colour change (PACC) is widely thought to be an adaptation to signal floral suitability to pollinators. Lotus filicaulis and Lotus sessilifolius are insect-pollinated herbaceous legumes with flowers that open yellow, shift to orange and finally red. This study examines the molecular basis for floral colour change in these Lotus species. Methods: Lotus filicaulis was cultivated in a glasshouse from which pollinating insects (bees) were excluded, and the rate of colour change was recorded in both unpollinated and manually pollinated flowers...
July 19, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28942180/de-novo-transcriptome-analysis-in-dendrobium-and-identification-of-critical-genes-associated-with-flowering
#3
Yue Chen, Qi Shen, Renan Lin, Zhuangliu Zhao, Chenjia Shen, Chongbo Sun
Artificial control of flowering time is pivotal for the ornamental value of orchids including the genus Dendrobium. Although various flowering pathways have been revealed in model plants, little information is available on the genetic regualtion of flowering in Dendrobium. To identify the critical genes associated with flowering, transcriptomes from four organs (leaf, root, stem and flower) of D. officinale were analyzed in our study. In total, 2645 flower-specific transcripts were identified. Functional annotation and classification suggested that several metabolic pathways, including four sugar-related pathways and two fatty acid-related pathways, were enriched...
September 14, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28936220/de-novo-assembly-of-the-camellia-nitidissima-transcriptome-reveals-key-genes-of-flower-pigment-biosynthesis
#4
Xingwen Zhou, Jiyuan Li, Yulin Zhu, Sui Ni, Jinling Chen, Xiaojuan Feng, Yunfeng Zhang, Shuangquan Li, Hongguang Zhu, Yuanguang Wen
The golden camellia, Camellia nitidissima Chi., is a well-known ornamental plant that is known as "the queen of camellias" because of its golden yellow flowers. The principal pigments in the flowers are carotenoids and flavonol glycosides. Understanding the biosynthesis of the golden color and its regulation is important in camellia breeding. To obtain a comprehensive understanding of flower development in C. nitidissima, a number of cDNA libraries were independently constructed during flower development. Using the Illumina Hiseq2500 platform, approximately 71...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28902884/development-of-est-ssr-markers-in-flowering-chinese-cabbage-brassica-campestris-l-ssp-chinensis-var-utilis-tsen-et-lee-based-on-de-novo-transcriptomic-assemblies
#5
Jingfang Chen, Ronghua Li, Yanshi Xia, Guihua Bai, Peiguo Guo, Zhiliang Wang, Hua Zhang, Kadambot H M Siddique
Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs)...
2017: PloS One
https://www.readbyqxmd.com/read/28844668/transcriptomic-analysis-of-flower-development-in-tea-camellia-sinensis-l
#6
Feng Liu, Yu Wang, Zhaotang Ding, Lei Zhao, Jun Xiao, Linjun Wang, Shibo Ding
Flowering is a critical and complicated process in plant development, involving interactions of numerous endogenous and environmental factors, but little is known about the complex network regulating flower development in tea plants. In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptomic analysis assembles gene-related information involved in reproductive growth of C. sinensis. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding...
October 5, 2017: Gene
https://www.readbyqxmd.com/read/28831055/horizontal-transfer-of-a-%C3%A3-1-6-glucanase-gene-from-an-ancestral-species-of-fungal-endophyte-to-a-cool-season-grass-host
#7
Hiroshi Shinozuka, Inoka K Hettiarachchige, Maiko Shinozuka, Noel O I Cogan, German C Spangenberg, Benjamin G Cocks, John W Forster, Timothy I Sawbridge
Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28830346/comparative-transcriptome-analysis-reveals-differentially-expressed-genes-associated-with-sex-expression-in-garden-asparagus-asparagus-officinalis
#8
Shu-Fen Li, Guo-Jun Zhang, Xue-Jin Zhang, Jin-Hong Yuan, Chuan-Liang Deng, Wu-Jun Gao
BACKGROUND: Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. RESULTS: De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds...
August 22, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28761813/rna-seq-data-from-different-developmental-stages-of-rafflesia-cantleyi-floral-buds
#9
Safoora Amini, Halimah Alias, Mohd Afiq Aizat-Juhari, Mohd-Noor Mat-Isa, Jumaat Haji Adam, Hoe-Han Goh, Kiew-Lian Wan
Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novo assembly of sequence reads...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28645249/comparative-transcriptomic-analysis-of-the-evolution-and-development-of-flower-size-in-saltugilia-polemoniaceae
#10
Jacob B Landis, Douglas E Soltis, Pamela S Soltis
BACKGROUND: Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators. RESULTS: Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28615048/integrated-metabolome-and-transcriptome-analysis-of-magnolia-champaca-identifies-biosynthetic-pathways-for-floral-volatile-organic-compounds
#11
Savitha Dhandapani, Jingjing Jin, Vishweshwaran Sridhar, Rajani Sarojam, Nam-Hai Chua, In-Cheol Jang
BACKGROUND: Magnolia champaca, commonly known as champak is a well-known tree due to its highly fragrant flowers. Champak floral scent is attributed to a complex mix of volatile organic compounds (VOCs). These aromatic flowers are widely used in flavors and fragrances industry. Despite its commercial importance, the VOC biosynthesis pathways in these flowers are largely unknown. Here, we combine metabolite and RNA sequencing (RNA-seq) analyses of fully opened champak flowers to discover the active VOC biosynthesis pathways as well as floral scent-related genes...
June 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28614366/de-novo-transcriptomic-analysis-and-development-of-est-ssrs-for-sorbus-pohuashanensis-hance-hedl
#12
Congcong Liu, Ying Dou, Xuelian Guan, Qiang Fu, Ze Zhang, Zenghui Hu, Jian Zheng, Yizeng Lu, Wei Li
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species...
2017: PloS One
https://www.readbyqxmd.com/read/28566222/tissue-specific-transcriptomic-profiling-provides-new-insights-into-the-reproductive-ecology-and-biology-of-the-iconic-seagrass-species-posidonia-oceanica
#13
Laura Entrambasaguas, Marlene Jahnke, Elio Biffali, Marco Borra, Remo Sanges, Lázaro Marín-Guirao, Gabriele Procaccini
Seagrasses form extensive meadows in shallow coastal waters and are among the world's most productive ecosystems. Seagrasses can produce both clonally and sexually, and flowering has long been considered infrequent, but important for maintaining genetically diverse stands. Here we investigate the molecular mechanisms involved in flowering of the seagrass Posidonia oceanica, an iconic species endemic to the Mediterranean. We generated a de novo transcriptome of this non-model species for leaf, male and female flower tissue of three individuals, and present molecular evidence for genes that may be involved in the flowering process and on the reproductive biology of the species...
May 26, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28535746/de-novo-transcriptome-analysis-and-glucosinolate-profiling-in-watercress-nasturtium-officinale-r-br
#14
Jin Jeon, Sun Ju Bong, Jong Seok Park, Young-Kyu Park, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi, Sang Un Park
BACKGROUND: Watercress (Nasturtium officinale R. Br.) is an aquatic herb species that is a rich source of secondary metabolites such as glucosinolates. Among these glucosinolates, watercress contains high amounts of gluconasturtiin (2-phenethyl glucosinolate) and its hydrolysis product, 2-phennethyl isothiocyanate, which plays a role in suppressing tumor growth. However, the use of N. officinale as a source of herbal medicines is currently limited due to insufficient genomic and physiological information...
May 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28512462/de-novo-transcriptome-profiling-of-flowers-flower-pedicels-and-pods-of-lupinus-luteus-yellow-lupine-reveals-complex-expression-changes-during-organ-abscission
#15
Paulina Glazinska, Waldemar Wojciechowski, Milena Kulasek, Wojciech Glinkowski, Katarzyna Marciniak, Natalia Klajn, Jacek Kesy, Jan Kopcewicz
Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28490318/integrated-mrna-and-microrna-transcriptome-variations-in-the-multi-tepal-mutant-provide-insights-into-the-floral-patterning-of-the-orchid-cymbidium-goeringii
#16
Fengxi Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qingquan Xu, Dan Huang, Chaoyi Zhao
BACKGROUND: Cymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants have considerable ecological and cultural value. However, the current understanding of the molecular mechanisms of floral patterning and multi-tepal development is limited. In this study, we performed expression profiling of both microRNA (miRNA) and mRNA from wild-type and typical multi-tepal-mutant flowers of C...
May 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28420173/transcriptome-sequencing-of-dianthus-spiculifolius-and-analysis-of-the-genes-involved-in-responses-to-combined-cold-and-drought-stress
#17
Aimin Zhou, Hongping Ma, Enhui Liu, Tongtong Jiang, Shuang Feng, Shufang Gong, Jingang Wang
Dianthus spiculifolius, a perennial herbaceous flower and a member of the Caryophyllaceae family, has strong resistance to cold and drought stresses. To explore the transcriptional responses of D. spiculifolius to individual and combined stresses, we performed transcriptome sequencing of seedlings under normal conditions or subjected to cold treatment (CT), simulated drought treatment (DT), or their combination (CTDT). After de novo assembly of the obtained reads, 112,015 unigenes were generated. Analysis of differentially expressed genes (DEGs) showed that 2026, 940, and 2346 genes were up-regulated and 1468, 707, and 1759 were down-regulated in CT, DT, and CTDT samples, respectively...
April 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28382950/diplosporous-development-in-boehmeria-tricuspis-insights-from-de-novo-transcriptome-assembly-and-comprehensive-expression-profiling
#18
Qing Tang, Gonggu Zang, Chaohua Cheng, Mingbao Luan, Zhigang Dai, Ying Xu, Zemao Yang, Lining Zhao, Jianguang Su
Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28361995/comparative-transcriptomic-analysis-of-vernalization-and-cytokinin-induced-floral-transition-in-dendrobium-nobile
#19
Zhenzhen Wen, Wenzhong Guo, Jinchi Li, Haisheng Lin, Chunmei He, Yunquan Liu, Qunyu Zhang, Wei Liu
Vernalization is required for floral initiation in Dendrobium. Interestingly, those beneficial effects can also be achieved by exogenous cytokinin application in greenhouses. Thus, an as yet unknown crosstalk/interaction may exist between vernalization and cytokinin signaling pathways. In this study, we showed, by de novo transcriptome assembly using RNA-seq data from both vegetative and reproductive tissue samples, that some floral transition-related genes-DnVRN1, FT, SOC1, LFY and AP1-were differentially expressed in low-temperature-challenged (LT) or thidiazuron (TDZ)-treated plants, compared to those mock-treated (CK)...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299441/the-r2r3myb-vvmybpa1-from-grape-reprograms-the-phenylpropanoid-pathway-in-tobacco-flowers
#20
Valentina Passeri, Stefan Martens, Elisabete Carvalho, Chantal Bianchet, Francesco Damiani, Francesco Paolocci
This work shows that, in tobacco, the ectopic expression of VvMYBPA1 , a grape regulator of proanthocyanidin biosynthesis, up- or down-regulates different branches of the phenylproanoid pathway, in a structure-specific fashion. Proanthocyanidins are flavonoids of paramount importance for animal and human diet. Research interest increasingly tilts towards generating crops enriched with these health-promoting compounds. Flavonoids synthesis is regulated by the MBW transcriptional complex, made of R2R3MYB, bHLH and WD40 proteins, with the MYB components liable for channeling the complex towards specific branches of the pathway...
August 2017: Planta
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