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https://www.readbyqxmd.com/read/29430358/comparative-de-novo-transcriptome-analysis-of-male-and-female-sea-buckthorn
#1
Ankush Bansal, Mehul Salaria, Tashil Sharma, Tsering Stobdan, Anil Kant
Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism...
February 2018: 3 Biotech
https://www.readbyqxmd.com/read/29398844/transcriptome-analysis-and-development-of-simple-sequence-repeat-ssr-markers-in-zingiber-striolatum-diels
#2
Kuanping Deng, Renju Deng, Jianxin Fan, Enfa Chen
Illumina-based paired-end sequencing technology was used for the high-throughput transcriptome sequencing of combined Zingiber striolatum Diels tissues (i.e., root, stem, leaf, flower, and fruit tissues). More than 130 million sequencing reads were generated, and a de novo assembly yielded 287,959 contigs and 112,107 unigenes with an average length of 1029 and 28,891 bp, respectively. Similarity searches with known sequences led to the identification of 51,804 (46.21%) genes. Of the annotated unigenes, 6867 and 51,987 were assigned to Gene Ontology and Clusters of Orthologous Groups categories, respectively...
February 2018: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29364900/de-novo-characterization-of-transcriptomes-from-two-north-american-papaipema-stem-borers-lepidoptera-noctuidae
#3
Sara J Oppenheim, Wiebke Feindt, Rob DeSalle, Paul Z Goldstein
Stem-borers in the genus Papaipema (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to specialists on more than 20 families of flowering plants, many of them highly toxic. Papaipema is the largest genus of noctuids endemic to North America and provides an excellent study system for the evolution of noctuid host plant use. To improve the availability of genomic resources for such investigations, we performed de novo transcriptome sequencing and assembly for two specialist Papaipema with unusual larval hosts: P...
2018: PloS One
https://www.readbyqxmd.com/read/29335419/a-global-view-of-transcriptome-dynamics-during-male-floral-bud-development-in-populus-tomentosa
#4
Zhong Chen, Pian Rao, Xiaoyu Yang, Xiaoxing Su, Tianyun Zhao, Kai Gao, Xiong Yang, Xinmin An
To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included 'response to environmental stimuli' and 'plant-type spore development'. One-third of the differentially expressed genes were transcription factors (TFs)...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29275214/de-novo-transcriptome-assembly-and-comparative-analysis-between-male-and-benzyladenine-induced-female-inflorescence-buds-of-plukenetia-volubilis
#5
Qiantang Fu, Longjian Niu, Mao-Sheng Chen, Yan-Bin Tao, Xiulan Wang, Huiying He, Bang-Zhen Pan, Zeng-Fu Xu
Plukenetia volubilis is a promising oilseed crop due to its seeds being rich in unsaturated fatty acids, especially alpha-linolenic acid. P. volubilis is monoecious, with separate male and female flowers on the same inflorescence. We previously reported that male flowers were converted to female flowers by exogenous cytokinin (6-benzyladenine, 6-BA) treatment in P. volubilis. To identify candidate genes associated with floral sex differentiation of P. volubilis, we performed de novo transcriptome assembly and comparative analysis on control male inflorescence buds (MIB) and female inflorescence buds (FIB) induced by 6-BA using Illumina sequencing technology...
December 9, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29261120/high-throughput-rna-seq-data-analysis-of-the-single-nucleotide-polymorphisms-snps-and-zygomorphic-flower-development-in-pea-pisum-sativum-l
#6
Keyuan Jiao, Xin Li, Wuxiu Guo, Shihao Su, Da Luo
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes...
December 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29258253/identification-of-the-sex-biased-gene-expression-and-putative-sex-associated-genes-in-eucommia-ulmoides-oliver-using-comparative-transcriptome-analyses
#7
Wencai Wang, Xianzhi Zhang
Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes...
December 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29233089/de-novo-transcriptome-assembly-from-flower-buds-of-dioecious-gynomonoecious-and-chemically-masculinized-female-coccinia-grandis-reveals-genes-associated-with-sex-expression-and-modification
#8
Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan Kumar Banerjee
BACKGROUND: Coccinia grandis (ivy gourd), is a dioecious member of Cucurbitaceae having heteromorphic sex chromosomes. Chromosome constitution of male and female plants of C. grandis is 22A + XY and 22A + XX respectively. Earlier we showed that a unique gynomonoecious form of C. grandis (22A + XX) also exists in nature bearing morphologically hermaphrodite flowers (GyM-H). Additionally, application of silver nitrate (AgNO3) on female plants induces stamen development leading to the formation of morphologically hermaphrodite flowers (Ag-H) despite the absence of Y-chromosome...
December 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29206203/de-novo-rna-sequencing-and-expression-analysis-of-aconitum-carmichaelii-to-analyze-key-genes-involved-in-the-biosynthesis-of-diterpene-alkaloids
#9
Megha Rai, Amit Rai, Noriaki Kawano, Kayo Yoshimatsu, Hiroki Takahashi, Hideyuki Suzuki, Nobuo Kawahara, Kazuki Saito, Mami Yamazaki
Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization...
December 5, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29166857/genome-analysis-of-the-foxtail-millet-pathogen-sclerospora-graminicola-reveals-the-complex-effector-repertoire-of-graminicolous-downy-mildews
#10
Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
BACKGROUND: Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches' broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S...
November 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29137608/the-pennycress-thlaspi-arvense-l-nectary-structural-and-transcriptomic-characterization
#11
Jason B Thomas, Marshall E Hampton, Kevin M Dorn, M David Marks, Clay J Carter
BACKGROUND: Pennycress [Thlaspi arvense L (Brassicaceae)] is being domesticated as a renewable biodiesel feedstock that also provides crucial ecosystems services, including as a nutritional resource for pollinators. However, its flowers produce significantly less nectar than other crop relatives in the Brassicaceae. This study was undertaken to understand the basic biology of the pennycress nectary as an initial step toward the possibility of enhancing nectar output from its flowers. RESULTS: Pennycress flowers contain four equivalent nectaries located extrastaminally at the base of the insertion sites of short and long stamens...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29068370/rna-seq-analysis-of-plant-maturity-in-crested-wheatgrass-agropyron-cristatum-l
#12
Fangqin Zeng, Bill Biligetu, Bruce Coulman, Michael P Schellenberg, Yong-Bi Fu
Crested wheatgrass (Agropyron cristatum L.) breeding programs aim to develop later maturing cultivars for extending early spring grazing in Western Canada. Plant maturity is a complex genetic trait, and little is known about genes associated with late maturity in this species. An attempt was made using RNA-Seq to profile the transcriptome of crested wheatgrass maturity and to analyze differentially expressed genes (DEGs) between early and late maturing lines. Three cDNA libraries for each line were generated by sampling leaves at the stem elongation stage, spikes at the boot and anthesis stages...
October 25, 2017: Genes
https://www.readbyqxmd.com/read/28992542/de-novo-transcriptome-sequencing-of-camellia-sasanqua-and-the-analysis-of-major-candidate-genes-related-to-floral-traits
#13
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...
November 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
#14
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...
October 17, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28942180/de-novo-transcriptome-analysis-in-dendrobium-and-identification-of-critical-genes-associated-with-flowering
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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