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de novo transcriptome flowering

Zheng Xiao, Jiale Su, Xiaobo Sun, Chang Li, Lisi He, Shangping Cheng, Xiaoqing Liu
Rhododendron molle G. Don occupies an important phylogenetic node in the genus rhododendron with unique yellow flower and medicinal functions. However, only limited genetic resources and their genome information are available for the generation of rhododendron flowers. The next generation sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provide a turning point for rhododendron research. Our goal is to use the genetic information to facilitate the relevant research on flowering and flower color formation in R...
June 2018: Genes & Genomics
Xiao-Di Hu, Bang-Zhen Pan, Qiantang Fu, Longjian Niu, Mao-Sheng Chen, Zeng-Fu Xu
BACKGROUND: Sacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil especially contains high amounts of α-linolenic acid (ALA), which is useful for the prevention of various diseases. However, little is known about the genetic information and genome sequence of Sacha Inchi, which has largely hindered functional genomics and molecular breeding studies...
May 22, 2018: BMC Genomics
Yunqing Cheng, Yuchu Zhang, Chunming Liu, Pengfei Ai, Jianfeng Liu
BACKGROUND: Hazel (Corylus spp.) exhibits ovary differentiation and development that is initiated from the ovary primordium after pollination, conferring the plant with a unique delayed fertilization. Failure of development of the ovary and ovule after pollination can lead to ovary abortion and blank fruit formation, respectively, with consequent yield loss. However, the genes involved in ovary and ovule differentiation and development are largely unknown. RESULTS: In unpollinated pistillate inflorescences (stage F), the stigma shows an extension growth pattern...
May 9, 2018: BMC Plant Biology
Luchao Sun, Amit Rai, Megha Rai, Michimi Nakamura, Noriaki Kawano, Kayo Yoshimatsu, Hideyuki Suzuki, Nobuo Kawahara, Kazuki Saito, Mami Yamazaki
The three Forsythia species, F. suspensa, F. viridissima and F. koreana, have been used as herbal medicines in China, Japan and Korea for centuries and they are known to be rich sources of numerous pharmaceutical metabolites, forsythin, forsythoside A, arctigenin, rutin and other phenolic compounds. In this study, de novo transcriptome sequencing and assembly was performed on these species. Using leaf and flower tissues of F. suspensa, F. viridissima and F. koreana, 1.28-2.45-Gbp sequences of Illumina based pair-end reads were obtained and assembled into 81,913, 88,491 and 69,458 unigenes, respectively...
May 7, 2018: Journal of Natural Medicines
Yun Xie, Xuewen Wang
Fruit yield is an important trait for horticultural crops. However, the limited fruit yield of Camellia chekiangoleosa, a novel promising oil tree, restricts the production of oil. The breeding improvement is little due to its long generation time and lack of available genomic sequence. We identified distinct fruit count phenotypes, high-yield (HY) and low-yield (LY). To understand the underlying genetic basis, we focused on global gene discovery and expression levels in floral buds, which affect fruit count...
April 27, 2018: Scientific Reports
Saneyoshi Ueno, Yukino Nakamura, Masaaki Kobayashi, Shin Terashima, Wataru Ishizuka, Kentaro Uchiyama, Yoshihiko Tsumura, Kentaro Yano, Susumu Goto
Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected transcriptome from the female and male flower, leaf, and inner bark. De novo assembly with 34.7 Gb of sequencing reads produced 158,542 transcripts from 69,618 loci, whose estimated coverage reached 95...
March 15, 2018: Plant & Cell Physiology
Chenghao Zhang, Wenqi Dong, Wei Gen, Baoyu Xu, Chenjia Shen, Chenliang Yu
Abelmoschus esculentus (okra or lady's fingers) is a vegetable with high nutritional value, as well as having certain medicinal effects. It is widely used as food, in the food industry, and in herbal medicinal products, but also as an ornamental, in animal feed, and in other commercial sectors. Okra is rich in bioactive compounds, such as flavonoids, polysaccharides, polyphenols, caffeine, and pectin. In the present study, the concentrations of total flavonoids and polysaccharides in five organs of okra were determined and compared...
February 27, 2018: Genes
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
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
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
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
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...
February 2018: Journal of Plant Physiology
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
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
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
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
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
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
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
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
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