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Nhan Trung Nguyen - One of the best experts on this subject based on the ideXlab platform.
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two ring opened oxetane taxoids containing a c 20 benzoyloxy group from the roots of taxus wallichiana zucc
Tetrahedron Letters, 2017Co-Authors: Phu Hoang Dang, Hanh H T Nguyen, Hien T T Truong, Truong Nhat Van Do, Hai X Nguyen, Mai Thanh Thi Nguyen, Manabu Abe, Ryukichi Takagi, Nhan Trung NguyenAbstract:Abstract Two new taxanes, named wallitaxane G ( 1 ) and H ( 2 ), were isolated from the roots of Taxus wallichiana (Taxaceae), together with nine known compounds ( 3 − 11 ). Their structures were elucidated on the basis of NMR spectroscopic analysis and the relative configurations of 1 and 2 were determined based on NOESY data. Wallitaxane H ( 2 ) showed the most potent α-glucosidase inhibitory activity, with an IC 50 value of 16.1 μM. Plausible biosynthetic pathways for the formation of 1 and 2 were proposed based on oxetane ring-opening and benzoyl migration.
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THE STUDY ON CHEMICAL CONSTITUENTS FROM THE NEEDLES OF TAXUS WALLICHIANA ZUCC. (Taxaceae)
Science and Technology Development Journal, 2009Co-Authors: Tam Thi Thanh Nguyen, Nhan Trung NguyenAbstract:A new taxane-type diterpene named 10-deacetyltaxuspine F (2) together with a known compound, taxuspine F (1), were isolated from the needles of Taxus wallichiana Zucc. (Taxaceae). Their chemical structures were elucidated by using spectroscopic methods and comparision with published data.
Pankaj Bhardwaj - One of the best experts on this subject based on the ideXlab platform.
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rnaseq based phylogenetic reconstruction of Taxaceae and cephaloTaxaceae
Cladistics, 2019Co-Authors: Aasim Majeed, Amandeep Singh, Shruti Choudhary, Pankaj BhardwajAbstract:Taxaceae and CephaloTaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within CephaloTaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq‐based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single‐copy complete orthologous groups were selected for phylogenetic analysis. Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and CephaloTaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within CephaloTaxaceae.
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RNAseq‐based phylogenetic reconstruction of Taxaceae and CephaloTaxaceae
Cladistics, 2018Co-Authors: Aasim Majeed, Amandeep Singh, Shruti Choudhary, Pankaj BhardwajAbstract:Taxaceae and CephaloTaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within CephaloTaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq‐based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single‐copy complete orthologous groups were selected for phylogenetic analysis. Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and CephaloTaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within CephaloTaxaceae.
Shu-miaw Chaw - One of the best experts on this subject based on the ideXlab platform.
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
Nature Publishing Group, 2019Co-Authors: Jie Liu, Shu-miaw Chaw, Yu-wen Chang, Lian-ming GaoAbstract:Abstract Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by “trnQ-IRs”. These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species
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Ancient Nuclear Plastid DNA in the Yew Family (Taxaceae)
Genome biology and evolution, 2014Co-Authors: Chih-yao Hsu, Shu-miaw ChawAbstract:Plastid-to-nucleus DNA transfer provides a rich genetic resource to the complexity of plant nuclear genome architecture. To date, the evolutionary route of nuclear plastid DNA (nupt) remain unknown in conifers. We have sequenced the complete plastomes of two yews, Amentotaxus formosana and Taxus mairei (Taxaceae of coniferales). Our comparative genomic analyses recovered an evolutionary scenario for plastomic reorganization from ancestral to extant plastomes in the three sampled Taxaceae genera, Amentotaxus, Cephalotaxus, and Taxus. Specific primers were designed to amplify nonsyntenic regions between ancestral and extant plastomes, and 12.6 kb of nupts were identified based on phylogenetic analyses. These nupts have significantly accumulated GC-to-AT mutations, reflecting a nuclear mutational environment shaped by spontaneous deamination of 5-methylcytosin. The ancestral initial codon of rps8 is retained in the T. nupts, but its corresponding extant codon is mutated and requires C-to-U RNA-editing. These findings suggest that nupts can help recover scenarios of the nucleotide mutation process. We show that the Taxaceae nupts we retrieved may have been retained because the Cretaceous and they carry information of both ancestral genomic organization and nucleotide composition, which offer clues for understanding the plastome evolution in conifers.
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Phylogeny of Taxaceae and CephaloTaxaceae Genera Inferred from Chloroplast matK Gene and Nuclear rDNA ITS Region
Molecular phylogenetics and evolution, 2000Co-Authors: Yuchang Cheng, Robert G Nicolson, Kim Tripp, Shu-miaw ChawAbstract: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).
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The phylogenetic positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia inferred from 18s rRNA sequences
Journal of molecular evolution, 1995Co-Authors: Shu-miaw Chaw, Huang Mo Sung, Huei Long, Andrey Zharkikh, Wen Hsiung LieAbstract:To determine the evolutionary positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia, we obtained 18S rRNA sequences from 11 new taxa representing the major living orders and families of gymnosperms. With the published Chlamydomonas as an outgroup, phylogenetic analyses of our new data and available sequences indicate that (1) the Gnetales form a monophyletic group, which is an outgroup to the conifers, (2) the conifers are monophyletic, (3) Taxaceae, CephaloTaxaceae, Cupressaceae, and Taxodiaceae form a monophyletic group, (4) Amentotaxus is closer to Torreya than to Cephalotaxus, suggesting that Amentotaxus is better to be classified as a member of Taxaceae, (5) Phyllocladus, Dacrycarpus, Podocarpus, and Nageia form a monophyletic group, and (6) Pinaceae is an outgroup to the other families of conifers. Our finding that Phyllocladus is a sister group of the Podocarpaceae disagrees with the suggestion that the phylloclade of the genus is an ancient structure and that the genus is a terminal taxon within the Podocarpaceae. The genus Nageia is more closely related to Podocarpus than to Dacrycarpus and was derived from within the Podocarpaceae. In conclusion, our data indicate that in conifers, the uniovulate cone occurred independently in Taxacaeae and CephaloTaxaceae, and in Podocarpaceae after the three families separated from Pinaceae, and support the hypothesis that the uniovulate cone is derived from reduction of a multiovulate cone.
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The phylogenetic position of Taxaceae based on 18S rRNA sequences.
Journal of molecular evolution, 1993Co-Authors: Shu-miaw Chaw, Huei Long, Andrey Zharkikh, Bin-shin Wang, Wen Hsiung LieAbstract:The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones.
Balkrishna Ghimire - One of the best experts on this subject based on the ideXlab platform.
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Comparative wood anatomy of Taxaceae
Australian Systematic Botany, 2015Co-Authors: Balkrishna Ghimire, Chunghee Lee, Kweon HeoAbstract:Comparative wood anatomy of Taxaceae s.l. was examined to elucidate the differences in wood features among genera. In total, 25 samples, comprising three varieties and seven species from five genera (Pseudotaxus was not included), were examined. Sliding microtome, wood maceration and scanning electron microscopy methods were used for the study. The growth rings are well developed and early and late wood are distinguishable in a cross-section. In general, there is remarkable uniformity in the characteristics of the five genera of Taxaceae, although some differences in quantitative traits were found. Wood of Taxaceae s.l. differs from that of most conifers by having helical thickening in the tracheid inner walls, with the exception of Austrotaxus spicata R.H.Compton. All genera are characterised by the absence of resin canals, predominantly uniseriate pits on the radial wall of the axial tracheids, and the presence of pits on the tangential walls of the axial tracheids. The rays are composed solely of parenchyma cells and are uniseriate (occasionally biseriate in Torreya nucifera (L.) Siebold et Zucc.), with a height of 1–22 cells. The genus Taxus shares more characteristics with Torreya than with Amentotaxus, Austrotaxus and Cephalotaxus. Correspondingly, Amentotaxus and Cephalotaxus resemble each other, marked by the presence of either diffuse or sparse axial parenchyma with nodulated transverse walls. Austrotaxus spicata is the sole species that lacks helical thickenings in the tracheid walls and has sparse axial parenchyma with smooth transverse walls. These two features, namely, the absence of helical thickenings and axial parenchyma with smooth transverse walls, are plesiomorphic and might be considered a more primitive character in wood anatomy. Among the other four genera, Amentotaxus appears to have an annular type of wall thickening that could be considered plesiomorphic to the spiral thickenings found in Taxus, Torreya and Cephalotaxus.
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Leaf anatomy and its implications for phylogenetic relationships in Taxaceae s. l.
Journal of Plant Research, 2014Co-Authors: Balkrishna GhimireAbstract:The comparative study on leaf anatomy and stomata structures of six genera of Taxaceae s . l . was conducted. Leaf anatomical structures were very comparable to each other in tissue shape and their arrangements. Taxus , Austrotaxus , and Pseudotaxus have no foliar resin canal, whereas Amentotaxus , Cephalotaxus , and Torreya have a single resin canal located below the vascular bundle. Among them, Torreya was unique with thick-walled, almost round sclerenchymatous epidermal cells. In addition, Amentotaxus and Torreya were comprised of some fiber cells around the vascular bundle. Also, Amentotaxus resembled Cephalotaxus harringtonia and its var. nana because they have discontinuous fibrous hypodermis. However, C . fortunei lacked the same kind of cells. Stomata were arranged in two stomatal bands separated by a mid-vein. The most unique stomatal structure was of Taxus with papillose accessory cells forming stomatal apparatus and of Torreya with deeply seated stomata covered with a special filament structure. Some morphological and molecular studies have already been discussed for the alternative classification of taxad genera into different minor families. The present study is also similar to these hypotheses because each genus has their own individuality in anatomical structure and stomata morphology. In conclusion, these differences in leaf and stomata morphology neither strongly support the two tribes in Taxaceae nor fairly recognize the monogeneric family, CephaloTaxaceae. Rather, it might support an alternative classification of taxad genera in different minor families or a single family Taxaceae including Cephalotaxus . In this study, we would prefer the latter one because there is no clear reason to separate Cephalotaxus from the rest genera of Taxaceae. Therefore, Taxaceae should be redefined with broad circumscriptions including Cephalotaxus .
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Cladistic analysis of Taxaceae s. l.
Plant Systematics and Evolution, 2014Co-Authors: Balkrishna GhimireAbstract:Taxaceae s. l. is a wider concept of classification treating five genera of Taxaceae s. str. and Cephalotaxus together. Cephalotaxus is morphologically very similar to the five genera of Taxaceae s. str. Various models of classification for six genera have already been published. However, the phylogenetic position and genuine relationships of these genera and species are still confusing. A cladistic analysis of Taxaceae s. l. has been carried out to resolve the problem existing in their phylogeny and to provide a new approach regarding the relationships of these six genera. Parsimony analyses were based on 28 characters and eight genera including two outgroups Agathis and Sciadopitys . The most parsimonious tree retained with branch length 38 and 194 rearrangement trials. Consistency index was 0.68 and retention index was 0.66. Principally, two main clades were found: one represented by Austrotaxus forming the base of the tree and another by the remaining five genera. Taxus + Pseudotaxus clade split after Austrotaxus , and Cephalotaxus was sister to Torreya + Amentotaxus clade. Taxus + Pseudotaxus clade was supported by the highest bootstrap value. Finally, cladistic analysis does not support existence of CephaloTaxaceae. Therefore, it would be better to classify Cephalotaxus within Taxaceae s. l. with the other five genera.
Aasim Majeed - One of the best experts on this subject based on the ideXlab platform.
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rnaseq based phylogenetic reconstruction of Taxaceae and cephaloTaxaceae
Cladistics, 2019Co-Authors: Aasim Majeed, Amandeep Singh, Shruti Choudhary, Pankaj BhardwajAbstract:Taxaceae and CephaloTaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within CephaloTaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq‐based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single‐copy complete orthologous groups were selected for phylogenetic analysis. Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and CephaloTaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within CephaloTaxaceae.
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RNAseq‐based phylogenetic reconstruction of Taxaceae and CephaloTaxaceae
Cladistics, 2018Co-Authors: Aasim Majeed, Amandeep Singh, Shruti Choudhary, Pankaj BhardwajAbstract:Taxaceae and CephaloTaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within CephaloTaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq‐based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single‐copy complete orthologous groups were selected for phylogenetic analysis. Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and CephaloTaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within CephaloTaxaceae.
