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de novo transcriptome flowering

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https://www.readbyqxmd.com/read/27855648/genome-and-transcriptome-sequencing-characterises-the-gene-space-of-macadamia-integrifolia-proteaceae
#1
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
#2
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
#3
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
#4
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...
October 24, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27764127/de-novo-sequencing-and-assembly-analysis-of-the-pseudostellaria-heterophylla-transcriptome
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/27673730/de-novo-transcriptome-assembly-databases-for-the-butterfly-orchid-phalaenopsis-equestris
#8
Shan-Ce Niu, Qing Xu, Guo-Qiang Zhang, Yong-Qiang Zhang, Wen-Chieh Tsai, Jui-Ling Hsu, Chieh-Kai Liang, Yi-Bo Luo, Zhong-Jian Liu
Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P...
September 27, 2016: Scientific Data
https://www.readbyqxmd.com/read/27635342/transcriptome-analysis-of-colored-calla-lily-zantedeschia-rehmannii-engl-by-illumina-sequencing-de-novo-assembly-annotation-and-est-ssr-marker-development
#9
Zunzheng Wei, Zhenzhen Sun, Binbin Cui, Qixiang Zhang, Min Xiong, Xian Wang, Di Zhou
Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. 'Rehmannii' using an Illumina HiSeq 2000 instrument. More than 59...
2016: PeerJ
https://www.readbyqxmd.com/read/27553669/de-novo-assembly-and-characterization-of-the-floral-transcriptome-of-an-economically-important-tree-species-lindera-glauca-lauraceae-including-the-development-of-est-ssr-markers-for-population-genetics
#10
Shanshan Zhu, Yanqian Ding, Zhaoyan Yap, Yingxiong Qiu
Lindera glauca (Lauraceae) is an economically important East Asian forest tree characterized by a dioecy in China and apomixis in Japan. However, patterns of population genetic diversity and structure of this species remain unknown for this species due to a lack of efficient molecular markers. In this study, we employed Illumina sequencing to analyze the transcriptomes of the female and male flower buds of L. glauca. We retrieved 59,753 and 75,075 unigenes for the female and male buds, respectively. Based on sequence similarity, 44,379 (74...
November 2016: Molecular Biology Reports
https://www.readbyqxmd.com/read/27542359/comparative-transcriptome-investigation-of-global-gene-expression-changes-caused-by-mir156-overexpression-in-medicago-sativa
#11
Ruimin Gao, Ryan S Austin, Lisa Amyot, Abdelali Hannoufa
BACKGROUND: Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic alfalfa plants overexpressing a precursor of alfalfa microRNA156 (MsmiR156) were recently generated by our group. These plants (miR156OE) showed enhanced biomass yield, reduced internodal length, increased shoot branching and trichome density, and a delay in flowering time. Transcripts of three SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes (MsSPL6, MsSPL12, and MsSPL13) were found to be targeted for cleavage by MsmiR156 in alfalfa...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27534116/cloning-and-functional-analysis-of-three-chalcone-synthases-from-the-flowers-of-safflowers-carthamus-tinctorius
#12
Junichi Shinozaki, Hiromichi Kenmoku, Kenichi Nihei, Kazuo Masuda, Masaaki Noji, Katsuhiro Konno, Yoshinori Asakawa, Kohei Kazuma
The flowers of safflowers (Carthamus tinctorius L.) are very important as they are the sole source of their distinct pigments, i.e. carthamus-red and -yellows, and have historically had strong connections to the cultural side of human activities such as natural dyes, rouge, and traditional medicines. The distinct pigments are quinochalcone C-glucosides, which are found specifically in the flowers of C. tinctorius. To investigate the biosynthetic pathways of quinochalcone C-glucosides, de novo assembly of the transcriptome was performed on the flowers using an Illumina sequencing platform to obtain 69,312 annotated coding DNA sequences...
June 2016: Natural Product Communications
https://www.readbyqxmd.com/read/27516339/rna-seq-based-evaluation-of-bicolor-tepal-pigmentation-in-asiatic-hybrid-lilies-lilium-spp
#13
Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
BACKGROUND: Color patterns in angiosperm flowers are produced by spatially and temporally restricted deposition of pigments. Identifying the mechanisms responsible for restricted pigment deposition is a topic of broad interest. Some dicots species develop bicolor petals, which are often caused by the post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. An Asiatic hybrid lily (Lilium spp.) cultivar Lollypop develops bicolor tepals with pigmented tips and white bases...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27486566/de-novo-sequencing-of-eucommia-ulmoides-flower-bud-transcriptomes-for-identification-of-genes-related-to-floral-development
#14
Huimin Liu, JianMin Fu, Hongyan Du, Jingjing Hu, Tana Wuyun
Eucommia ulmoides Oliver is a woody perennial dioecious species native to China and has great economic value. However, little is known about flower bud development in this species. In this study, the transcriptomes of female and male flower buds were sequenced using the Illumina platform, a next-generation sequencing technology that provides cost-effective, highly efficient transcriptome profiling. In total, 11,558,188,080 clean reads were assembled into 75,065 unigenes with an average length of 1011 bp by de novo assembly using Trinity software...
September 2016: Genomics Data
https://www.readbyqxmd.com/read/27242839/different-gene-expression-patterns-between-leaves-and-flowers-in-lonicera-japonica-revealed-by-transcriptome-analysis
#15
Libin Zhang, Yan Long, Chunhua Fu, Jun Xiang, Jianping Gan, Gang Wu, Haibo Jia, Longjiang Yu, Maoteng Li
The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27216755/de-novo-transcriptome-analysis-in-radish-raphanus-sativus-l-and-identification-of-critical-genes-involved-in-bolting-and-flowering
#16
Shanshan Nie, Chao Li, Liang Xu, Yan Wang, Danqiong Huang, Everlyne M Muleke, Xiaochuan Sun, Yang Xie, Liwang Liu
BACKGROUND: The appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq)...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27206631/the-floral-transcriptomes-of-four-bamboo-species-bambusoideae-poaceae-support-for-common-ancestry-among-woody-bamboos
#17
William P Wysocki, Eduardo Ruiz-Sanchez, Yanbin Yin, Melvin R Duvall
BACKGROUND: Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events. RESULTS: Transcriptomes were assembled using both reference-based and de novo methods...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27142449/the-first-de-novo-transcriptome-of-pepino-solanum-muricatum-assembly-comprehensive-analysis-and-comparison-with-the-closely-related-species-s-caripense-potato-and-tomato
#18
Francisco J Herraiz, José Blanca, Pello Ziarsolo, Pietro Gramazio, Mariola Plazas, Gregory J Anderson, Jaime Prohens, Santiago Vilanova
BACKGROUND: Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution...
2016: BMC Genomics
https://www.readbyqxmd.com/read/26981408/de-novo-transcriptome-assembly-of-two-contrasting-pumpkin-cultivars
#19
Aliki Xanthopoulou, Fotis Psomopoulos, Ioannis Ganopoulos, Maria Manioudaki, Athanasios Tsaftaris, Irini Nianiou-Obeidat, Panagiotis Madesis
Cucurbita pepo (squash, pumpkin, gourd), a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq) of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, 'Big Moose' with large round fruits and 'Munchkin' with small round fruits, were harvested for total RNA extraction...
March 2016: Genomics Data
https://www.readbyqxmd.com/read/26964333/-transcriptome-analysis-of-bioenergy-plant-miscanthus-sinensis-anderss-by-rna-seq
#20
Xian Zhang, Jianhong Wang, Man Yu, Kai Cao, Li Zhuang, Changxu Xu, Weidong Cao
Miscanthus sinensis Anderss is a perennial C4-grass. It is a promising bioenergy plant, which has been proposed as general feedstock for biomass and lignocellulosic biofuel production. In this study, the flower and leaf buds transcriptomes of Miscanthus sinensis Anderss were sequenced by the platform of Illumina HiSeq 2000. In total 98 326 Unigenes were generated by de novo assembly with an average length of 822 bp and N50 of 1 023 bp. Based on the NR, NT, Swiss-Prot, KEGG, GO and COG databases (Evalue < le-5), 74 134 (75...
October 2015: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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