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Fei Qiao - One of the best experts on this subject based on the ideXlab platform.

  • evaluation of reference genes for normalizing rt qpcr in leaves and suspension cells of cephalotaxus hainanensis under various stimuli
    Plant Methods, 2019
    Co-Authors: Huapeng Sun, Xuefei Jiang, Hanqing Cong, Mengli Sun, Fei Qiao
    Abstract:

    Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. Cephalotaxus hainanensis is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it. In this study, 9 candidate reference genes were selected from the transcriptome data of C. hainanensis; 3 statistical algorithms (geNorm, NormFinder, BestKeeper) were applied to evaluate their expression stabilities through 180 samples under 6 stimuli treatments in leaves and leaf-derived suspension cultured cells; a comprehensive stabilities ranking was also performed by RefFinder. The results showed that suitable reference genes in C. hainanensis should be selected for normalization relative to different experimental sets. 18S showed a higher stability than other candidate reference genes which ranked at the top two suitable genes under all experimental setups in this study. This study is the first to evaluate the stability of reference genes in C. hainanensis and supply an important foundation to use the RT-qPCR for an accurate and far-reaching gene expression analysis in C. hainanensis.

  • Evaluation of reference genes for normalizing RT-qPCR in leaves and suspension cells of Cephalotaxus hainanensis under various stimuli
    'Springer Science and Business Media LLC', 2019
    Co-Authors: Huapeng Sun, Xuefei Jiang, Hanqing Cong, Mengli Sun, Fei Qiao
    Abstract:

    Abstract Background Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. Cephalotaxus hainanensis is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it. Results In this study, 9 candidate reference genes were selected from the transcriptome data of C. hainanensis; 3 statistical algorithms (geNorm, NormFinder, BestKeeper) were applied to evaluate their expression stabilities through 180 samples under 6 stimuli treatments in leaves and leaf-derived suspension cultured cells; a comprehensive stabilities ranking was also performed by RefFinder. The results showed that suitable reference genes in C. hainanensis should be selected for normalization relative to different experimental sets. 18S showed a higher stability than other candidate reference genes which ranked at the top two suitable genes under all experimental setups in this study. Conclusion This study is the first to evaluate the stability of reference genes in C. hainanensis and supply an important foundation to use the RT-qPCR for an accurate and far-reaching gene expression analysis in C. hainanensis

  • de novo characterization of a cephalotaxus hainanensis transcriptome and genes related to paclitaxel biosynthesis
    PLOS ONE, 2014
    Co-Authors: Fei Qiao, Xuefei Jiang, Hanqing Cong, Rongxiang Wang, Junmei Yin, Dan Qian, Zhunian Wang, Peter Nick
    Abstract:

    Cephalotaxus hainanensis, an endangered plant, is known to contain several metabolites with anti-cancer activity. Despite its clinical impact, the alkaloid metabolism of this species has remained largely uncharacterized. The potential of Cephalotaxus for metabolic engineering of medically interesting compounds has, so far, not been exploited, due to the almost complete lack of molecular information. We have therefore performed a high throughput RNA-seq analysis and assembled the transcriptome de novo. Raw reads comprising 4.3 Gbp were assembled de novo into 39,416 unique sequences (unigenes) with a mean length of 1,089.8 bp and a total assembly size of 45.8 Mbp, which equals to more than 50 times the number of Cephalotaxaceae sequences currently deposited in the GenBank (as of August 2013). As proof of principle for medically interesting pathways, gene fragments related to paclitaxel biosynthesis were searched and detected. To verify their functionality, the metabolic product paclitaxel, and its precursor baccatin III, were identified in the leaves of C. hainanensis by HPLC, and shown to be induced by MeJA. This finding demonstrates exemplarily the potential of the annotated transcriptome as information resource for the biotechnological exploitation of plant secondary metabolism.

Ting Wang - One of the best experts on this subject based on the ideXlab platform.

  • phylogeography of cephalotaxus oliveri Cephalotaxaceae in relation to habitat heterogeneity physical barriers and the uplift of the yungui plateau
    Molecular Phylogenetics and Evolution, 2014
    Co-Authors: Chunbo Wang, Ting Wang
    Abstract:

    Habitat heterogeneity, physical barriers, and the uplift of the Yungui Plateau were found to deeply affect the phylogeographic pattern and evolutionary history of Cephalotaxus oliveri, a perennial conifer endemic to China. In this study, we explored the phylogeography using three chloroplast sequences (trnL-trnF, trnT-trnD and atpB-rbcL) in 22 natural populations of C. oliveri distributed throughout its range. The Yungui Plateau populations of C. oliveri were revealed to origin ca. 9.15Ma by molecular clock estimation, which is consistent with rapid uplift of the Qinghai-Tibetan Plateau (QTP) ca. 8-10Ma. Additionally, geological effects of the Yungui Plateau were suggested to promote the rapid intra-specific differentiation of C. oliveri in the Pliocene and Early Pleistocene. The relatively low level of genetic diversity (h=0.719, θ=1.17×10(-3)) and high population differentiation (NST=0.771 and GST=0.642) implied restricted gene flow among populations, which was confirmed by the Nested Clade Analysis (NCA). Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion. Furthermore, the statistical dispersal-vicariance analysis indicated that the center of origin was in Central China. The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia during the Pleistocene ice ages. Our results highlighted that habitat heterogeneity and physical barriers presenting in a species range can predict genetic patterns.

  • the complete chloroplast genome sequence of cephalotaxus oliveri Cephalotaxaceae evolutionary comparison of cephalotaxus chloroplast dnas and insights into the loss of inverted repeat copies in gymnosperms
    Genome Biology and Evolution, 2013
    Co-Authors: Xuan Yi, Bo Wang, Yingjuan Su, Ting Wang
    Abstract:

    We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

  • development of microsatellite loci for cephalotaxus oliveri Cephalotaxaceae and cross amplification in cephalotaxus
    American Journal of Botany, 2011
    Co-Authors: Huawei Pan, Yingrong Guo, Ting Wang
    Abstract:

    PREMISE OF THE STUDY: Microsatellite loci were developed for Cephalotaxus oliveri, an endemic and endangered conifer in China, which will allow assessment of the levels of genetic diversity and a means to understand the genetic consequences of habitat fragmentation. METHODS AND RESULTS: Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) Repeats protocol, 19 microsatellite loci were identified in C. oliveri, 13 of which were polymorphic within a sample of 52 individuals representing five natural populations. The actual number of alleles per locus ranged from one to five. Twelve polymorphic loci were also successfully amplified in C. fortunei. CONCLUSIONS: These microsatellite loci will provide a useful tool for further investigating genetic variation in natural populations of C. oliveri, which will inform future conservation and management strategies. Additionally, cross-amplification in C. fortunei suggested the potential utility of these loci in this and other congeneric species.

Shu Miaw Chaw - One of the best experts on this subject based on the ideXlab platform.

  • Phylogeny of Taxaceae and Cephalotaxaceae Genera Inferred from Chloroplast matK Gene and Nuclear rDNA ITS Region
    Molecular phylogenetics and evolution, 2000
    Co-Authors: Yuchang Cheng, Robert G Nicolson, Kim Tripp, Shu Miaw Chaw
    Abstract:

    Phylogeny of the Taxaceae genera and the monotypic family Cephalotaxaceae has been extraordinarily controversial. In this paper chloroplast matK genes and nuclear ITS sequences were determined for all six genera of the two families and representatives of other conifer families. Analysis using either the nonsynonymous sites or the deduced amino acid sequences of matK genes strongly indicates that taxad genera and Cephalotaxaceae are monophyletic, with the Taxodiaceae/Cupressaceae clade as their sister group. Cephalotaxus is basal to the taxad genera, among which two clades, Torreya/Amentotaxus and Taxus/Pseudotaxus/Austrotaxus, are resolved. They correspond to Janchen's two tribes, Torreyeae and Taxeae. In Taxeae, Austrotaxus is the first to branch off. Analyses of the nuclear ITS sequence data corroborated the topology of the matK gene tree. These results refute the views that Cephalotaxaceae has no alliance with Taxaceae and that Austrotaxus and Amentotaxus should be excluded from the Taxaceae. We estimated the divergence time between the Taxodiaceae/Cupressaceae and the Cephalotaxaceae/Taxaceae clades to be 192-230 Myr ago and the divergence time between taxads and Cephalotaxus to be 149-179 Myr ago. Soon after the latter divergence event, within 6-8 Myr, the two taxad tribes originated. In conclusion, our data do not support Florin's claim that taxads could be traced to Devonian psilophytes (359-395 Myr ago).

  • Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.
    Molecular Biology and Evolution, 1997
    Co-Authors: Shu Miaw Chaw, Andrey Zharkikh, Huang Mo Sung, Tak Cheung Lau
    Abstract:

    To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and angiosperms was analyzed using the neighbor-joining and maximum-parsimony methods. With Selaginella as the outgroup, the analysis strongly indicates that the seed plants form a monophyletic group with the ferns as a sister group. Within the seed plants the angiosperms are clearly a monophyletic group. Although the bootstrap support for the monophyly of the gymnosperm clade is moderate, the monophyly is further supported by its lack of angiosperm-specific indels. Within the gymnosperms there appear to be three monophyletic clades: Cycadales-Ginkgoales, Gnetales, and Coniferales. The cycad-ginkgo clade is the earliest gymnosperm lineage. Given the strong support for the sister group relationship between Gnetales and Coniferales, it is unlikely that Gnetales is a sister group of the angiosperms, contrary to the view of many plant taxonomists. Within Coniferales, Pinaceae is monophyletic and basal to the remaining conifer families, among which there are three monophyletic clades: Phyllocladaceae-Podocarpaceae, Araucariaceae, and Sciadopityaceae-Taxaceae-Cephalotaxaceae-Taxodiacea e-Cupressaceae. Within the latter clade, Sciadopityaceae may be an outgroup to the other four families. Among the angiosperms, no significant cluster at the level of subclass was found, but there was evidence that Nymphaeaceae branched off first. Within the remaining angiosperms, the monocots included in this study are nested and form a monophyletic group. This study attests to the utility of nuclear 18S rRNA sequences in addressing relationships among living gymnosperms. Considerable variation in substitution rates was observed among the ferns and seed plants.

Xiao-quan Wang - One of the best experts on this subject based on the ideXlab platform.

  • Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes
    PLOS ONE, 2014
    Co-Authors: Ying Lu, Zu-yu Yang, Xiao-quan Wang
    Abstract:

    Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

  • Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes
    2014
    Co-Authors: Jin-hua Ran, Zu-yu Yang, Dong-mei Guo, Xiao-quan Wang
    Abstract:

    Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older tha

Bastien Nay - One of the best experts on this subject based on the ideXlab platform.

  • geographic locality greatly influences fungal endophyte communities in cephalotaxus harringtonia
    Fungal Biology, 2013
    Co-Authors: Aude Langenfeld, Bastien Nay, Soizic Prado, Corine Cruaud, Sandrine Lacoste, Edith Bury, Francois Hachette, Tsuyoshi Hosoya, Joelle Dupont
    Abstract:

    Although endophytes of conifers have been extensively studied, few data are available on Cephalotaxaceae. We examined foliar and stem endophytes of Cephalotaxus harringtonia, within its natural range in Japan and outside its natural range in France to study the effect of geography on endophyte community composition. In Japan, rapidly growing endophytes were dominant and may have masked the real diversity, in comparison to France where most endophytes were growing slowly. Analyses of ITS rDNA revealed 104 different Blast Groups among 554 isolates. Almost no overlap between endophyte assemblages of C. harringtonia from the two countries was observed. It seems that Japanese C. harringtonia trees, which should be well adapted to their native site, would host a specific, endemic endophyte community, while trees that have been introduced recently to a foreign site, in France, should have captured existing cosmopolitan and more generalist taxa. In Japan the majority of xylariaceous taxa, which dominated the communities, were unknown and, although closely related to Asian taxa, may be new to science. Dothideomycetes were more prevalent in France. Locally, urban environment, particularly in Japan, may have introduced some perturbations in the native endophyte community of C. harringtonia, with an abundance of generalist fungi such as Nigrospora and Colletotrichum.

  • natural products from cephalotaxus sp chemical diversity and synthetic aspects
    Natural Product Reports, 2012
    Co-Authors: Hajer Abdelkafi, Bastien Nay
    Abstract:

    The Cephalotaxus genus belongs to the Cephalotaxaceae family of conifers. Over the past decades it has proved to be a fruitful source of interesting natural products, especially alkaloids (cephalotaxine esters) and terpenoids (abietanes, troponoids), which often display medicinal properties, especially in the anticancer area. Homoharringtonine is active against some orphan leukaemia and is nowadays approaching marketability. A phytochemical update will be provided and the total synthesis of alkaloids and terpenoids will be discussed in detail.

  • natural products from cephalotaxus sp chemical diversity and synthetic aspects
    Natural Product Reports, 2012
    Co-Authors: Hajer Abdelkafi, Bastien Nay
    Abstract:

    Covering: up to 2012 The Cephalotaxus genus belongs to the Cephalotaxaceae family of conifers. Over the past decades it has proved to be a fruitful source of interesting natural products, especially alkaloids (cephalotaxine esters) and terpenoids (abietanes, troponoids), which often display medicinal properties, especially in the anticancer area. Homoharringtonine is active against some orphan leukaemia and is nowadays approaching marketability. A phytochemical update will be provided and the total synthesis of alkaloids and terpenoids will be discussed in detail.