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de novo transcriptome flowering

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https://www.readbyqxmd.com/read/28299441/the-r2r3myb-vvmybpa1-from-grape-reprograms-the-phenylpropanoid-pathway-in-tobacco-flowers
#1
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...
March 15, 2017: Planta
https://www.readbyqxmd.com/read/28298915/transcriptomic-analysis-reveals-mechanisms-of-sterile-and-fertile-flower-differentiation-and-development-in-viburnum-macrocephalum-f-keteleeri
#2
Zhaogeng Lu, Jing Xu, Weixing Li, Li Zhang, Jiawen Cui, Qingsong He, Li Wang, Biao Jin
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28287176/de-novo-and-reference-transcriptome-assembly-of-transcripts-expressed-during-flowering-provide-insight-into-seed-setting-in-tetraploid-red-clover
#3
Mallikarjuna Rao Kovi, Helga Amdahl, Muath Alsheikh, Odd Arne Rognli
Red clover (Trifolium pratense L.) is one of the most important legume forage species in temperate livestock agriculture. Tetraploid red clover cultivars are generally producing less seed than diploid cultivars. Improving the seed setting potential of tetraploid cultivars is necessary to utilize the high forage quality and environmentally sustainable nitrogen fixation ability of red clover. In the current study, our aim was to identify candidate genes involved in seed setting. Two genotypes, 'Tripo' with weak seed setting and 'Lasang' with strong seed setting were selected for transcriptome analysis...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253862/de-novo-transcriptome-assembly-reveals-high-transcriptional-complexity-in-pisum-sativum-axillary-buds-and-shows-rapid-changes-in-expression-of-diurnally-regulated-genes
#4
Stephanie C Kerr, Federico Gaiti, Christine A Beveridge, Milos Tanurdzic
BACKGROUND: The decision for a bud to grow into a branch is a key regulatory process affecting plant architecture. In order to study molecular processes regulating axillary bud outgrowth in the model plant garden pea (Pisum sativum), we sequenced the axillary bud transcriptome and performed de novo transcriptome assembly. RESULTS: We assembled a pea axillary bud transcriptome into 81,774 transcripts comprised of 194,067 isoforms. This new pea transcriptome resource is both comprehensive and representative, as shown by comparison to other available pea sequence resources...
March 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28250432/transcriptomic-analyses-reveal-biosynthetic-genes-related-to-rosmarinic-acid-in-dracocephalum-tanguticum
#5
Huie Li, Yaru Fu, Hao Sun, Yanfu Zhang, Xiaozhong Lan
Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28241786/de-novo-sequencing-and-comparative-transcriptome-analysis-of-the-male-and-hermaphroditic-flowers-provide-insights-into-the-regulation-of-flower-formation-in-andromonoecious-taihangia-rupestris
#6
Weiguo Li, Lihui Zhang, Zhan Ding, Guodong Wang, Yandi Zhang, Hongmei Gong, Tianjun Chang, Yanwen Zhang
BACKGROUND: Taihangia rupestris, an andromonoecious plant species, bears both male and hermaphroditic flowers within the same individual. However, the establishment and development of male and hermaphroditic flowers in andromonoecious Taihangia remain poorly understood, due to the limited genetic and sequence information. To investigate the potential molecular mechanism in the regulation of Taihangia flower formation, we used de novo RNA sequencing to compare the transcriptome profiles of male and hermaphroditic flowers at early and late developmental stages...
February 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#7
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28225035/deep-sequencing-and-transcriptome-analyses-to-identify-genes-involved-in-secoiridoid-biosynthesis-in-the-tibetan-medicinal-plant-swertia-mussotii
#8
Yue Liu, Yi Wang, Fengxian Guo, Lin Zhan, Toni Mohr, Prisca Cheng, Naxin Huo, Ronghui Gu, Danning Pei, Jiaqing Sun, Li Tang, Chunlin Long, Luqi Huang, Yong Q Gu
Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties effective in the treatment of various ailments including hepatitis. Secoiridoids are the major bioactive compounds in S. mussotii. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from the root, leaf, stem, and flower tissues, and performed de novo sequence assembly, yielding 98,613 unique transcripts with an N50 of 1,085 bp. Putative functions could be assigned to 35,029 transcripts (35...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28180085/de-novo-transcriptome-assembly-of-heavy-metal-tolerant-silene-dioica
#9
Radim Cegan, Vojtech Hudzieczek, Roman Hobza
Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) database with the accession number SRP094611...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28141906/genomic-evidence-of-gene-flow-during-reinforcement-in-texas-phlox
#10
Federico Roda, Fábio K Mendes, Matthew W Hahn, Robin Hopkins
Gene flow can impede the evolution of reproductive isolating barriers between species. Reinforcement is the process by which pre-zygotic reproductive isolation evolves in sympatry due to selection to decrease costly hybridization. It is known that reinforcement can be prevented by too much gene flow, but we still do not know how often have pre-zygotic barriers evolved in the presence of gene flow or how much gene flow can occur during reinforcement. Flower color divergence in the native Texas wildflower, Phlox drummondii, is one of the best-studied cases of reinforcement...
January 31, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28068903/comparative-transcriptome-analysis-reveals-candidate-genes-for-the-biosynthesis-of-natural-insecticide-in-tanacetum-cinerariifolium
#11
Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Kumar Shukla, Sumit Ghosh, Vikrant Gupta, Suchitra Banerjee, Laiq Ur Rahman
BACKGROUND: Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties. Despite such advantages of commercial value coming with the eco-friendly tag, most enzymes/genes involved in the pyrethrin biosynthesis pathway remain unidentified and uncharacterized. Since the flowers of Tanacetum cinerariifolium are rich in major pyrethrins, next generation transcriptome sequencing was undertaken to compare the flowers and the leaves of the plant de novo to identify differentially expressed transcripts and ascertain which among them might be involved in and responsible for the differential accumulation of pyrethrins in T...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068432/transcriptome-analysis-of-leaves-flowers-and-fruits-perisperm-of-coffea-arabica-l-reveals-the-differential-expression-of-genes-involved-in-raffinose-biosynthesis
#12
Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito Dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protasio Pereira
Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads...
2017: PloS One
https://www.readbyqxmd.com/read/27995074/de-novo-transcriptome-assembly-of-the-mycoheterotrophic-plant-monotropa-hypopitys
#13
Alexey V Beletsky, Mikhail A Filyushin, Eugeny V Gruzdev, Alexander M Mazur, Egor B Prokhortchouk, Elena Z Kochieva, Andrey V Mardanov, Nikolai V Ravin, Konstantin G Skryabin
Monotropa hypopitys (pinesap) is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27855648/genome-and-transcriptome-sequencing-characterises-the-gene-space-of-macadamia-integrifolia-proteaceae
#14
Catherine J Nock, Abdul Baten, Bronwyn J Barkla, Agnelo Furtado, Robert J Henry, Graham J King
BACKGROUND: The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information...
November 17, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27833829/de-novo-transcriptome-sequencing-and-comparative-analysis-to-discover-genes-related-to-floral-development-in-cymbidium-faberi-rolfe
#15
Yuying Sun, Guangdong Wang, Yuxia Li, Li Jiang, Yuxia Yang, Shuangxue Guan
Cymbidium faberi is a traditional orchid flower in China that is highly appreciated for its fragrant aroma from its zygomorphic flowers. One bottleneck of the commercial production of C. faberi is the long vegetative growth phase of the orchid and the difficulty of the regulation of its flowering time. Moreover, its flower size, shape and color are often targeting traits for orchid breeders. Understanding the molecular mechanisms of floral development in C. faberi will ultimately benefit the genetic improvement of this orchid plant...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27829354/transcriptome-sequencing-and-metabolite-analysis-for-revealing-the-blue-flower-formation-in-waterlily
#16
Qian Wu, Jie Wu, Shan-Shan Li, Hui-Jin Zhang, Cheng-Yong Feng, Dan-Dan Yin, Ru-Yan Wu, Liang-Sheng Wang
BACKGROUND: Waterlily (Nymphaea spp.), a perennial herbaceous aquatic plant, is divided into two ecological groups: hardy waterlily and tropical waterlily. Although the hardy waterlily has no attractive blue flower cultivar, its adaptability is stronger than tropical waterlily because it can survive a cold winter. Thus, breeding hardy waterlily with real blue flowers has become an important target for breeders. Molecular breeding may be a useful way. However, molecular studies on waterlily are limited due to the lack of sequence data...
November 9, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27778293/deep-analysis-of-wild-vitis-flower-transcriptome-reveals-unexplored-genome-regions-associated-with-sex-specification
#17
Miguel Jesus Nunes Ramos, João Lucas Coito, Joana Fino, Jorge Cunha, Helena Silva, Patrícia Gomes de Almeida, Maria Manuela Ribeiro Costa, Sara Amâncio, Octávio S Paulo, Margarida Rocheta
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp...
January 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/27764127/de-novo-sequencing-and-assembly-analysis-of-the-pseudostellaria-heterophylla-transcriptome
#18
Jun Li, Wei Zhen, Dengkai Long, Ling Ding, Anhui Gong, Chenghong Xiao, Weike Jiang, Xiaoqing Liu, Tao Zhou, Luqi Huang
Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P...
2016: PloS One
https://www.readbyqxmd.com/read/27716052/de-novo-assembly-and-transcriptome-characterization-of-spruce-dwarf-mistletoe-arceuthobium-sichuanense-uncovers-gene-expression-profiling-associated-with-plant-development
#19
Yonglin Wang, Xuewu Li, Weifen Zhou, Tao Li, Chengming Tian
BACKGROUND: The parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spruce dwarf mistletoe, SDM) infects Qinghai spruce (Picea crassifolia) and causes severe damage to spruce forests in Northwest China. SDM is a Chinese native parasitic plant and acquires carbohydrates and mineral nutrition from its hosts. However, underlying molecular basis of the physiological development is largely unknown...
October 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27677333/unravelling-molecular-mechanisms-from-floral-initiation-to-lipid-biosynthesis-in-a-promising-biofuel-tree-species-pongamia-pinnata-using-transcriptome-analysis
#20
Rachapudi V Sreeharsha, Shalini Mudalkar, Kambam T Singha, Attipalli R Reddy
Pongamia pinnata (L.) (Fabaceae) is a promising biofuel tree species which is underexploited in the areas of both fundamental and applied research, due to the lack of information either on transcriptome or genomic data. To investigate the possible metabolic pathways, we performed whole transcriptome analysis of Pongamia through Illumina NextSeq platform and generated 2.8 GB of paired end sequence reads. The de novo assembly of raw reads generated 40,000 contigs and 35,000 transcripts, representing leaf, flower and seed unigenes...
September 28, 2016: Scientific Reports
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