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Akemi Ohmiya - One of the best experts on this subject based on the ideXlab platform.

  • generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next generation sequencing technology
    BMC Genomics, 2017
    Co-Authors: Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori, Akemi Ohmiya
    Abstract:

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of Chrysanthemums, we read expressed sequence tags (ESTs) of Chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3′-UTR, and 5′-UTR cDNAs derived from various tissues of Chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our Chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in Chrysanthemums. We confirmed that our Chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in Chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of Chrysanthemums including the myriad cultivars at the molecular level.

  • Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology
    BMC, 2017
    Co-Authors: Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori, Akemi Ohmiya
    Abstract:

    Abstract Background Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. Results To obtain useful information about molecular bases for floral traits of Chrysanthemums, we read expressed sequence tags (ESTs) of Chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3′-UTR, and 5′-UTR cDNAs derived from various tissues of Chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our Chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in Chrysanthemums. Conclusion We confirmed that our Chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in Chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of Chrysanthemums including the myriad cultivars at the molecular level

  • carotenoid cleavage dioxygenase cmccd4a contributes to white color formation in Chrysanthemum petals
    Plant Physiology, 2006
    Co-Authors: Akemi Ohmiya, Ryutaro Aida, Sanae Kishimoto, Satoshi Yoshioka, Katsuhiko Sumitomo
    Abstract:

    The white petals of Chrysanthemum (Chrysanthemum morifolium Ramat.) are believed to contain a factor that inhibits the accumulation of carotenoids. To find this factor, we performed polymerase chain reaction-Select subtraction screening and obtained a clone expressed differentially in white and yellow petals. The deduced amino acid sequence of the protein (designated CmCCD4a) encoded by the clone was highly homologous to the sequence of carotenoid cleavage dioxygenase. All the white-flowered Chrysanthemum cultivars tested showed high levels of CmCCD4a transcript in their petals, whereas most of the yellow-flowered cultivars showed extremely low levels. Expression of CmCCD4a was strictly limited to flower petals and was not detected in other organs, such as the root, stem, or leaf. White petals turned yellow after the RNAi construct of CmCCD4a was introduced. These results indicate that in white petals of Chrysanthemums, carotenoids are synthesized but are subsequently degraded into colorless compounds, which results in the white color.

  • regulation of carotenoid biosynthesis in petals and leaves of Chrysanthemum Chrysanthemum morifolium
    Physiologia Plantarum, 2006
    Co-Authors: Sanae Kishimoto, Akemi Ohmiya
    Abstract:

    We analyzed carotenoid composition and the content and expression of genes encoding isoprenoid and carotenoid biosynthetic enzymes in petals and leaves of Chrysanthemums. Most of the carotenoids in yellow petals were β,ɛ-carotenoids, lutein and its derivatives, reflecting the high expression levels of lycopene ɛ-cyclase (LCYE). In contrast, the ratio of β,β-carotenoids to total carotenoids in leaves were higher than that of β,ɛ-carotenoids, reflecting the high expression levels of lycopen β-cyclase (LCYB). Petals of the yellow-flowered cultivar Yellow Paragon showed increased accumulation and drastic componential changes of carotenoids as they matured. In petals of the white-flowered cultivar Paragon, carotenoid content was drastically decreased during petal development and became less than the detection limit late in development. Transcript levels of most genes tested increased during petal development in Yellow Paragon. All genes except that for 1-deoxyxylulose 5-phosphate synthase (DXS) showed similar expression patterns in Paragon. Between-cultivar comparison of the expression of these genes in the petals at mid-development showed no distinct differences between petal color. It is possible that the formation of white petal color is due to neither down-regulation nor destruction of the carotenoid biosynthetic pathway. We presume that another factor inhibits carotenoid accumulation in Chrysanthemum petals.

  • transformation of Chrysanthemum with mutated ethylene receptor genes mdg ers1 transgenes conferring reduced ethylene sensitivity and characterization of the transformants
    Postharvest Biology and Technology, 2005
    Co-Authors: Takako Narumi, R Aida, Akemi Ohmiya, Shigeru Satoh
    Abstract:

    Abstract We generated mutated ethylene receptor genes ( mDG-ERS1 s) from the Chrysanthemum ethylene receptor (DG-ERS1) cDNA by introducing one-nucleotide substitutions corresponding to those present in Arabidopsis etr1-1 , etr1-2 , etr1-3 , and etr1-4 and tomato Nr . The promoter of a tobacco elongation factor 1α (EF1α) gene was fused to DG-ERS1 cDNA or one of the mDG-ERS1 s. The resulting constructs were named EF1α∷mDG-ERS1(etr1-1) , - ERS1(etr1-2) and so on, and introduced into Chrysanthemum cv. Sei-Marine. We obtained putative transformants resistant to an antibiotic paromomycin with a yield of 2.4–6.2% depending on the construct. The mDG-ERS1(etr1-4) construct tended to be more effective in conferring reduced ethylene sensitivity in Chrysanthemum than the others. PCR analysis gave amplification corresponding to a partial sequence of EF1α∷mDG-ERS1 transgenes. Southern blot analysis showed that, in the mDG-ERS1(etr1-4) transformant, not only the lines with reduced sensitivity to ethylene but also those sensitive to ethylene harbored the mDG-ERS1(etr1-4) transgene. The present results showed the usefulness of mutated ethylene receptor genes mDG-ERS1 s for generation of transgenic Chrysanthemums with reduced ethylene sensitivity.

Fadi Chen - One of the best experts on this subject based on the ideXlab platform.

  • Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata
    'Springer Science and Business Media LLC', 2021
    Co-Authors: Lina Liu, Sumei Chen, Fadi Chen, Weimin Fang, Ye Liu, Zhiyong Guan
    Abstract:

    Abstract Background Chrysanthemum (Chrysanthemum morifolium) black spot disease caused by Alternaria alternata is one of the plant’s most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes to analyze the potential interaction mechanism between the two species, i.e., host and pathogen. Results C. morifolium and A. alternata were subjected to dual RNA-seq at 1, 12, and 24 h after inoculation, and differential expression genes (DEGs) in both species were identified. This analysis confirmed 153,532 DEGs in Chrysanthemum and 14,932 DEGs in A. alternata, which were involved in plant-fungal interactions and phytohormone signaling. Fungal DEGs such as toxin synthesis related enzyme and cell wall degrading enzyme genes played important roles during Chrysanthemum infection. Moreover, a series of key genes highly correlated with the early, middle, or late infection stage were identified, together with the regulatory network of key genes annotated in the Plant Resistance Genes database (PRGdb) or Pathogen-Host Interactions database (PHI-base). Highly correlated genes were identified at the late infection stage, expanding our understanding of the interplay between C. morifolium and A. alternata. Additionally, six DEGs each from Chrysanthemum and A. alternata were selected for quantitative real-time PCR (qRT-PCR) assays to validate the RNA-seq output. Conclusions Collectively, data obtained in this study enriches the resources available for research into the interactions that exist between Chrysanthemum and A. alternata, thereby providing a theoretical basis for the development of new Chrysanthemum cultivars with resistance to pathogen

  • transcriptomic and hormone analyses reveal mechanisms underlying petal elongation in Chrysanthemum morifolium jinba
    Plant Molecular Biology, 2017
    Co-Authors: Jingjing Wang, Sumei Chen, Aiping Song, Jiafu Jiang, Haibin Wang, Lian Ding, Feng Shen, Fadi Chen
    Abstract:

    Key message Auxin regulates Chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate Chrysanthemum petal elongation.

  • transcriptome wide identification and expression profiling of the dof transcription factor gene family in Chrysanthemum morifolium
    Frontiers in Plant Science, 2016
    Co-Authors: Aiping Song, Sumei Chen, Zhiyong Guan, Tianwei Gao, Jingjing Xin, Qingqing Fan, Kunkun Zhao, Fadi Chen
    Abstract:

    The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species Chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and Chrysanthemum and six pairs of paralogous proteins in Chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and Chrysanthemum were analysed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5’ RLM-RACE to map the cleavage sites in CmDOF3, 15 and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.

  • identification of Chrysanthemum Chrysanthemum morifolium self incompatibility
    The Scientific World Journal, 2014
    Co-Authors: Fan Wang, Fadi Chen, Weimin Fang, Fengjiao Zhang, Nianjun Teng
    Abstract:

    There has been a heated argument over self-incompatibilityof Chrysanthemum (Chrysanthemum morifolium) among Chrysanthemum breeders. In order to solve the argument, we investigated pistil receptivity, seed set, and compatible index of 24 Chrysanthemum cultivars. It was found that the 24 cultivars averagely had 3.7–36.3 pollen grains germinating on stigmas at 24 hours after self-pollination through the fluorescence microscope using aniline blue staining method. However, only 10 of them produced self-pollinated seeds, and their seed sets and compatible indexes were 0.03–56.50% and 0.04–87.50, respectively. The cultivar “Q10-33-1” had the highest seed set (56.50%) and compatible index (87.50), but ten of its progeny had a wide range of separation in seed set (0–37.23%) and compatible index (0–68.65). The results indicated that most of Chrysanthemum cultivars were self-incompatible, while a small proportion of cultivars were self-compatible. In addition, there is a comprehensive separation of self-incompatibility among progeny from the same self-pollinated self-compatible Chrysanthemum cultivar. Therefore, it is better to emasculate inflorescences during Chrysanthemum hybridization breeding when no information concerning its self-incompatibility characteristics is available. However, if it is self-incompatible and propagated by vegetative methods, it is unnecessary to carry out emasculation when it is used as a female plant during hybridization breeding.

  • changes in leaf morphology antioxidant activity and photosynthesis capacity in two different drought tolerant cultivars of Chrysanthemum during and after water stress
    Scientia Horticulturae, 2013
    Co-Authors: Jing Sun, Fadi Chen, Aiping Song, Jun Zeng, Shuang Han, Weimin Fang, Jiafu Jiang, Sumei Chen
    Abstract:

    Abstract Two Chrysanthemum cultivars, drought tolerant ‘Nannong Xuefeng’ and drought sensitive ‘Nannong Jingyan’ were subjected to 7-day drought stress by withholding irrigation, followed by re-watering for 3 days. We analyzed the biomass, morphological characteristics, physiological changes, and transcription profiles of genes involved in reactive oxygen species (ROS) scavenging. The biomass of ‘Nannong Xuefeng’ increased 67.5% by 7-day drought, while little increase was observed in drought sensitive ‘Nannong Jingyan’. It showed that ‘Nannong Xuefeng’ had denser trichomes, lower stomata density and greater quantities of wax on leaf surfaces, i.e., 2.3- and 3-fold of wax in ‘Nannong Jingyan’, respectively. Leaves of ‘Nannong Jingyan’ had a higher concentration of superoxide anion radicals, malondialdehyde, and proline, however, these indicators in ‘Nannong Xuefeng’ were stable throughout the duration of drought stress and rehydration. Other important factors leading to drought tolerance in Chrysanthemums are associated with reduced ROS damage; these factors include higher activities of antioxidant enzymes, such as SOD (EC 1.15.1.1), POD (EC 1.11.1.7), and CAT (EC 1.11.1.6), and induced expression of genes encoding these enzymes and APX (EC1.11.1.11). Although stomatal conductance, net photosynthetic rate, transpiration rate, chlorophyll concentration, and chlorophyll fluorescence of the two cultivars both decreased with the reduced soil water content, the decreases occurred earlier and were more apparent in ‘Nannong Jingyan’ that in ‘Nannong Jingyan’. In addition, ‘Nannong Xuefeng’ had a higher photosynthetic capacity during the stress. Our findings provide new insights into the mechanisms of drought tolerance in Chrysanthemum plants.

Sumei Chen - One of the best experts on this subject based on the ideXlab platform.

  • Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata
    'Springer Science and Business Media LLC', 2021
    Co-Authors: Lina Liu, Sumei Chen, Fadi Chen, Weimin Fang, Ye Liu, Zhiyong Guan
    Abstract:

    Abstract Background Chrysanthemum (Chrysanthemum morifolium) black spot disease caused by Alternaria alternata is one of the plant’s most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes to analyze the potential interaction mechanism between the two species, i.e., host and pathogen. Results C. morifolium and A. alternata were subjected to dual RNA-seq at 1, 12, and 24 h after inoculation, and differential expression genes (DEGs) in both species were identified. This analysis confirmed 153,532 DEGs in Chrysanthemum and 14,932 DEGs in A. alternata, which were involved in plant-fungal interactions and phytohormone signaling. Fungal DEGs such as toxin synthesis related enzyme and cell wall degrading enzyme genes played important roles during Chrysanthemum infection. Moreover, a series of key genes highly correlated with the early, middle, or late infection stage were identified, together with the regulatory network of key genes annotated in the Plant Resistance Genes database (PRGdb) or Pathogen-Host Interactions database (PHI-base). Highly correlated genes were identified at the late infection stage, expanding our understanding of the interplay between C. morifolium and A. alternata. Additionally, six DEGs each from Chrysanthemum and A. alternata were selected for quantitative real-time PCR (qRT-PCR) assays to validate the RNA-seq output. Conclusions Collectively, data obtained in this study enriches the resources available for research into the interactions that exist between Chrysanthemum and A. alternata, thereby providing a theoretical basis for the development of new Chrysanthemum cultivars with resistance to pathogen

  • transcriptomic and hormone analyses reveal mechanisms underlying petal elongation in Chrysanthemum morifolium jinba
    Plant Molecular Biology, 2017
    Co-Authors: Jingjing Wang, Sumei Chen, Aiping Song, Jiafu Jiang, Haibin Wang, Lian Ding, Feng Shen, Fadi Chen
    Abstract:

    Key message Auxin regulates Chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate Chrysanthemum petal elongation.

  • transcriptome wide identification and expression profiling of the dof transcription factor gene family in Chrysanthemum morifolium
    Frontiers in Plant Science, 2016
    Co-Authors: Aiping Song, Sumei Chen, Zhiyong Guan, Tianwei Gao, Jingjing Xin, Qingqing Fan, Kunkun Zhao, Fadi Chen
    Abstract:

    The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species Chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and Chrysanthemum and six pairs of paralogous proteins in Chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and Chrysanthemum were analysed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5’ RLM-RACE to map the cleavage sites in CmDOF3, 15 and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.

  • changes in leaf morphology antioxidant activity and photosynthesis capacity in two different drought tolerant cultivars of Chrysanthemum during and after water stress
    Scientia Horticulturae, 2013
    Co-Authors: Jing Sun, Fadi Chen, Aiping Song, Jun Zeng, Shuang Han, Weimin Fang, Jiafu Jiang, Sumei Chen
    Abstract:

    Abstract Two Chrysanthemum cultivars, drought tolerant ‘Nannong Xuefeng’ and drought sensitive ‘Nannong Jingyan’ were subjected to 7-day drought stress by withholding irrigation, followed by re-watering for 3 days. We analyzed the biomass, morphological characteristics, physiological changes, and transcription profiles of genes involved in reactive oxygen species (ROS) scavenging. The biomass of ‘Nannong Xuefeng’ increased 67.5% by 7-day drought, while little increase was observed in drought sensitive ‘Nannong Jingyan’. It showed that ‘Nannong Xuefeng’ had denser trichomes, lower stomata density and greater quantities of wax on leaf surfaces, i.e., 2.3- and 3-fold of wax in ‘Nannong Jingyan’, respectively. Leaves of ‘Nannong Jingyan’ had a higher concentration of superoxide anion radicals, malondialdehyde, and proline, however, these indicators in ‘Nannong Xuefeng’ were stable throughout the duration of drought stress and rehydration. Other important factors leading to drought tolerance in Chrysanthemums are associated with reduced ROS damage; these factors include higher activities of antioxidant enzymes, such as SOD (EC 1.15.1.1), POD (EC 1.11.1.7), and CAT (EC 1.11.1.6), and induced expression of genes encoding these enzymes and APX (EC1.11.1.11). Although stomatal conductance, net photosynthetic rate, transpiration rate, chlorophyll concentration, and chlorophyll fluorescence of the two cultivars both decreased with the reduced soil water content, the decreases occurred earlier and were more apparent in ‘Nannong Jingyan’ that in ‘Nannong Jingyan’. In addition, ‘Nannong Xuefeng’ had a higher photosynthetic capacity during the stress. Our findings provide new insights into the mechanisms of drought tolerance in Chrysanthemum plants.

  • next generation sequencing of the Chrysanthemum nankingense asteraceae transcriptome permits large scale unigene assembly and ssr marker discovery
    PLOS ONE, 2013
    Co-Authors: Haibin Wang, Sumei Chen, Aiping Song, Weimin Fang, Jiafu Jiang, Zhiyong Guan, Hui Peng, Yuan Liao, Fadi Chen
    Abstract:

    Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

Aiping Song - One of the best experts on this subject based on the ideXlab platform.

  • the Chrysanthemum nankingense genome provides insights into the evolution and diversification of Chrysanthemum flowers and medicinal traits
    Molecular Plant, 2018
    Co-Authors: Chi Song, Aiping Song, Yifei Liu, Gangqiang Dong, Hongbo Zhao, Wei Sun, Shyam Ramakrishnan, Ying Wang, Shuaibin Wang, Yan Niu
    Abstract:

    Abstract The Asteraceae (Compositae), a large plant family of approximately 24 000–35 000 species, accounts for ∼10% of all angiosperm species and contributes a lot to plant diversity. The most representative members of the Asteraceae are the economically important Chrysanthemums (Chrysanthemum L.) that diversified through reticulate evolution. Biodiversity is typically created by multiple evolutionary mechanisms such as whole-genome duplication (WGD) or polyploidization and locally repetitive genome expansion. However, the lack of genomic data from Chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification. Here, we used Oxford Nanopore long-read technology to sequence the diploid Chrysanthemum nankingense genome, which represents one of the progenitor genomes of domesticated Chrysanthemums. Our analysis revealed that the evolution of the C. nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recent WGD that distinguishes Chrysanthemum from sunflower, which diverged from Chrysanthemum approximately 38.8 million years ago. Variations of ornamental and medicinal traits in Chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication. Collectively, our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of Chrysanthemum plants, and also to accelerate their breeding and improvement.

  • transcriptomic and hormone analyses reveal mechanisms underlying petal elongation in Chrysanthemum morifolium jinba
    Plant Molecular Biology, 2017
    Co-Authors: Jingjing Wang, Sumei Chen, Aiping Song, Jiafu Jiang, Haibin Wang, Lian Ding, Feng Shen, Fadi Chen
    Abstract:

    Key message Auxin regulates Chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate Chrysanthemum petal elongation.

  • transcriptome wide identification and expression profiling of the dof transcription factor gene family in Chrysanthemum morifolium
    Frontiers in Plant Science, 2016
    Co-Authors: Aiping Song, Sumei Chen, Zhiyong Guan, Tianwei Gao, Jingjing Xin, Qingqing Fan, Kunkun Zhao, Fadi Chen
    Abstract:

    The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species Chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and Chrysanthemum and six pairs of paralogous proteins in Chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and Chrysanthemum were analysed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5’ RLM-RACE to map the cleavage sites in CmDOF3, 15 and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.

  • changes in leaf morphology antioxidant activity and photosynthesis capacity in two different drought tolerant cultivars of Chrysanthemum during and after water stress
    Scientia Horticulturae, 2013
    Co-Authors: Jing Sun, Fadi Chen, Aiping Song, Jun Zeng, Shuang Han, Weimin Fang, Jiafu Jiang, Sumei Chen
    Abstract:

    Abstract Two Chrysanthemum cultivars, drought tolerant ‘Nannong Xuefeng’ and drought sensitive ‘Nannong Jingyan’ were subjected to 7-day drought stress by withholding irrigation, followed by re-watering for 3 days. We analyzed the biomass, morphological characteristics, physiological changes, and transcription profiles of genes involved in reactive oxygen species (ROS) scavenging. The biomass of ‘Nannong Xuefeng’ increased 67.5% by 7-day drought, while little increase was observed in drought sensitive ‘Nannong Jingyan’. It showed that ‘Nannong Xuefeng’ had denser trichomes, lower stomata density and greater quantities of wax on leaf surfaces, i.e., 2.3- and 3-fold of wax in ‘Nannong Jingyan’, respectively. Leaves of ‘Nannong Jingyan’ had a higher concentration of superoxide anion radicals, malondialdehyde, and proline, however, these indicators in ‘Nannong Xuefeng’ were stable throughout the duration of drought stress and rehydration. Other important factors leading to drought tolerance in Chrysanthemums are associated with reduced ROS damage; these factors include higher activities of antioxidant enzymes, such as SOD (EC 1.15.1.1), POD (EC 1.11.1.7), and CAT (EC 1.11.1.6), and induced expression of genes encoding these enzymes and APX (EC1.11.1.11). Although stomatal conductance, net photosynthetic rate, transpiration rate, chlorophyll concentration, and chlorophyll fluorescence of the two cultivars both decreased with the reduced soil water content, the decreases occurred earlier and were more apparent in ‘Nannong Jingyan’ that in ‘Nannong Jingyan’. In addition, ‘Nannong Xuefeng’ had a higher photosynthetic capacity during the stress. Our findings provide new insights into the mechanisms of drought tolerance in Chrysanthemum plants.

  • next generation sequencing of the Chrysanthemum nankingense asteraceae transcriptome permits large scale unigene assembly and ssr marker discovery
    PLOS ONE, 2013
    Co-Authors: Haibin Wang, Sumei Chen, Aiping Song, Weimin Fang, Jiafu Jiang, Zhiyong Guan, Hui Peng, Yuan Liao, Fadi Chen
    Abstract:

    Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

Katsutomo Sasaki - One of the best experts on this subject based on the ideXlab platform.

  • generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next generation sequencing technology
    BMC Genomics, 2017
    Co-Authors: Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori, Akemi Ohmiya
    Abstract:

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of Chrysanthemums, we read expressed sequence tags (ESTs) of Chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3′-UTR, and 5′-UTR cDNAs derived from various tissues of Chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our Chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in Chrysanthemums. We confirmed that our Chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in Chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of Chrysanthemums including the myriad cultivars at the molecular level.

  • generation of gene edited Chrysanthemum morifolium using multicopy transgenes as targets and markers
    Plant and Cell Physiology, 2017
    Co-Authors: Mitsuko Kishikaboshi, Ryutaro Aida, Katsutomo Sasaki
    Abstract:

    The most widely used gene editing technology-the CRISPR/Cas9 system-employs a bacterial monomeric DNA endonuclease known as clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) and single-guide RNA (sgRNA) that directs Cas9 to a complementary target DNA. However, introducing mutations into higher polyploid plant species, especially for species without genome information, has been difficult. Chrysanthemum morifolium (Chrysanthemum) is one of the most important ornamental plants, but it is a hexaploid with a large genome; moreover, it lacks whole-genome information. These characteristics hinder genome editing in Chrysanthemum. In the present study, we attempted to perform gene editing using the CRISPR/Cas9 system to introduce mutations into Chrysanthemum. We constructed transgenic Chrysanthemum plants expressing the yellowish-green fluorescent protein gene from Chiridius poppei (CpYGFP) and targeted CpYGFP for gene editing. We compared the activity of a Cauliflower mosaic virus (CaMV) 35S promoter and parsley ubiquitin promoter in Chrysanthemum calli and chose the parsley ubiquitin promoter to drive Cas9. We selected two sgRNAs to target different positions in the CpYGFP gene and obtained transgenic calli containing mutated CpYGFP genes (CRISPR-CpYGFP-Chrysanthemum). A DNA sequencing analysis and fluorescence observations indicated that cells containing the mutated CpYGFP gene grew independently of cells containing the original CpYGFP gene in one callus. We finally obtained the CRISPR-CpYGFP-Chrysanthemum shoot containing a mutation in the CpYGFP sequence. This is the first report of gene editing using the CRISPR/Cas9 system in Chrysanthemum and sheds light on Chrysanthemum genome editing.

  • Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology
    BMC, 2017
    Co-Authors: Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori, Akemi Ohmiya
    Abstract:

    Abstract Background Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. Results To obtain useful information about molecular bases for floral traits of Chrysanthemums, we read expressed sequence tags (ESTs) of Chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3′-UTR, and 5′-UTR cDNAs derived from various tissues of Chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our Chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in Chrysanthemums. Conclusion We confirmed that our Chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in Chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of Chrysanthemums including the myriad cultivars at the molecular level