当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae).

Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae).

Abstract：

:The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defined from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for differences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Wang X,Ye X,Zhao L,Li D,Guo Z,Zhuang H

doi

10.1038/s41598-017-11367-x

subject

Has Abstract

pub_date

2017-09-14 00:00:00

pages

11546

issue

1

issn

2045-2322

pii

10.1038/s41598-017-11367-x

journal_volume

7

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • Multiple genotypes of Echovirus 11 circulated in mainland China between 1994 and 2017.

    abstract：:Echovirus 11 (E-11) is one of the most frequently isolated enteroviruses causing meningitis and other diseases such as hand, foot, and mouth disease (HFMD) and acute flaccid paralysis (AFP). Fifty-nine newly determined E-11 VP1 sequences from the China AFP and HFMD surveillance network and 500 E-11 VP1 sequences obtai...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-46870-w

    authors： Li J,Yan D,Chen L,Zhang Y,Song Y,Zhu S,Ji T,Zhou W,Gan F,Wang X,Hong M,Guan L,Shi Y,Wu G,Xu W

    更新日期：2019-07-22 00:00:00

  • Coronary micro-computed tomography angiography in mice.

    abstract：:Coronary computed tomography angiography is an established technique in clinical practice and a valuable tool in the diagnosis of coronary artery disease in humans. Imaging of coronaries in preclinical research, i.e. in small animals, is very difficult due to the high demands on spatial and temporal resolution. Mice e...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-73735-4

    authors： Sawall S,Beckendorf J,Amato C,Maier J,Backs J,Vande Velde G,Kachelrieß M,Kuntz J

    更新日期：2020-10-08 00:00:00

  • Selection of the optimal intensity normalization region for FDG-PET studies of normal aging and Alzheimer's disease.

    abstract：:The primary method for measuring brain metabolism in humans is positron emission tomography (PET) imaging using the tracer 18F-fluorodeoxyglucose (FDG). Standardized uptake value ratios (SUVR) are commonly calculated from FDG-PET images to examine intra- and inter-subject effects. Various reference regions are used in...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-65957-3

    authors： Nugent S,Croteau E,Potvin O,Castellano CA,Dieumegarde L,Cunnane SC,Duchesne S

    更新日期：2020-06-09 00:00:00

  • Lactate is a potent inhibitor of the capsaicin receptor TRPV1.

    abstract：:Tissue ischemia results in an accumulation of lactate and local or systemic lactic acidosis. In nociceptive sensory neurons, lactate was reported to sensitize or activate the transient receptor potential ion channel TRPA1 and acid-sensing ion channels (ASICs). However, it is unclear how lactate modulates the TRPV1 reg...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep36740

    authors： de la Roche J,Walther I,Leonow W,Hage A,Eberhardt M,Fischer M,Reeh PW,Sauer S,Leffler A

    更新日期：2016-11-09 00:00:00

  • Abiotic stressors impact outer membrane vesicle composition in a beneficial rhizobacterium: Raman spectroscopy characterization.

    abstract：:Outer membrane vesicles (OMVs) produced by Gram-negative bacteria have roles in cell-to-cell signaling, biofilm formation, and stress responses. Here, the effects of abiotic stressors on OMV contents and composition from biofilm cells of the plant health-promoting bacterium Pseudomonas chlororaphis O6 (PcO6) are exami...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-78357-4

    authors： Potter M,Hanson C,Anderson AJ,Vargis E,Britt DW

    更新日期：2020-12-04 00:00:00

  • Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children.

    abstract：:Viral upper respiratory tract infection (URTI) predisposes to bacterial pneumonia possibly by facilitating growth of bacteria such as Streptococcus pneumoniae colonising the nasopharynx. We investigated whether viral URTI is temporally associated with an increase in nasopharyngeal pneumococcal concentration. Episodes ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-29119-w

    authors： Morpeth SC,Munywoki P,Hammitt LL,Bett A,Bottomley C,Onyango CO,Murdoch DR,Nokes DJ,Scott JAG

    更新日期：2018-07-23 00:00:00

  • Direct nitrogen fixation at the edges of graphene nanoplatelets as efficient electrocatalysts for energy conversion.

    abstract：:Nitrogen fixation is essential for the synthesis of many important chemicals (e.g., fertilizers, explosives) and basic building blocks for all forms of life (e.g., nucleotides for DNA and RNA, amino acids for proteins). However, direct nitrogen fixation is challenging as nitrogen (N₂) does not easily react with other ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep02260

    authors： Jeon IY,Choi HJ,Ju MJ,Choi IT,Lim K,Ko J,Kim HK,Kim JC,Lee JJ,Shin D,Jung SM,Seo JM,Kim MJ,Park N,Dai L,Baek JB

    更新日期：2013-01-01 00:00:00

  • Observation of strongly enhanced photoluminescence from inverted cone-shaped silicon nanostructures. [corrected].

    abstract：:Silicon nanowires (SiNWs) attached to a wafer substrate are converted to inversely tapered silicon nanocones (SiNCs). After excitation with visible light, individual SiNCs show a 200-fold enhanced integral band-to-band luminescence as compared to a straight SiNW reference. Furthermore, the reverse taper is responsible...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep17089

    authors： Schmitt SW,Sarau G,Christiansen S

    更新日期：2015-11-26 00:00:00

  • A Comparison of the Antibacterial and Antifungal Activities of Thiosulfinate Analogues of Allicin.

    abstract：:Allicin (diallylthiosulfinate) is a defence molecule from garlic (Allium sativum L.) with broad antimicrobial activities in the low µM range against Gram-positive and -negative bacteria, including antibiotic resistant strains, and fungi. Allicin reacts with thiol groups and can inactivate essential enzymes. However, a...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-25154-9

    authors： Leontiev R,Hohaus N,Jacob C,Gruhlke MCH,Slusarenko AJ

    更新日期：2018-04-30 00:00:00

  • Immature particles and capsid-free viral RNA produced by Yellow fever virus-infected cells stimulate plasmacytoid dendritic cells to secrete interferons.

    abstract：:Plasmacytoid dendritic cells (pDCs) are specialized in the production of interferons (IFNs) in response to viral infections. The Flaviviridae family comprises enveloped RNA viruses such as Hepatitis C virus (HCV) and Dengue virus (DENV). Cell-free flaviviridae virions poorly stimulate pDCs to produce IFN. By contrast,...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-29235-7

    authors： Sinigaglia L,Gracias S,Décembre E,Fritz M,Bruni D,Smith N,Herbeuval JP,Martin A,Dreux M,Tangy F,Jouvenet N

    更新日期：2018-07-18 00:00:00

  • Inhibition of Lysyl Oxidases Improves Drug Diffusion and Increases Efficacy of Cytotoxic Treatment in 3D Tumor Models.

    abstract：:Tumors are characterized by a rigid, highly cross-linked extracellular matrix (ECM), which impedes homogeneous drug distribution and potentially protects malignant cells from exposure to therapeutics. Lysyl oxidases are major contributors to tissue stiffness and the elevated expression of these enzymes observed in mos...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep17576

    authors： Schütze F,Röhrig F,Vorlová S,Gätzner S,Kuhn A,Ergün S,Henke E

    更新日期：2015-12-01 00:00:00

  • An Aqueous-Based Approach for Fabrication of PVDF/MWCNT Porous Composites.

    abstract：:In this paper, we demonstrate the fabrication of conductive porous polymers based on foaming of an aqueous dispersion of polymeric particles and multi-walled carbon nanotubes (CNT). By tuning the surface energy of the constituents, we direct their preferential adsorption at the air-liquid (bubble) interface or within ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-01770-9

    authors： Rezvantalab H,Ghazi N,Ambrusch MJ,Infante J,Shojaei-Zadeh S

    更新日期：2017-05-11 00:00:00

  • Efficient derivation of knock-out and knock-in rats using embryos obtained by in vitro fertilization.

    abstract：:Rats are effective model animals and have contributed to the development of human medicine and basic research. However, the application of reproductive engineering techniques to rats is not as advanced compared with mice, and genome editing in rats has not been achieved using embryos obtained by in vitro fertilization...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-47964-1

    authors： Honda A,Tachibana R,Hamada K,Morita K,Mizuno N,Morita K,Asano M

    更新日期：2019-08-09 00:00:00

  • Antibody-mediated enhancement aggravates chikungunya virus infection and disease severity.

    abstract：:The arthropod-transmitted chikungunya virus (CHIKV) causes a flu-like disease that is characterized by incapacitating arthralgia. The re-emergence of CHIKV and the continual risk of new epidemics have reignited research in CHIKV pathogenesis. Virus-specific antibodies have been shown to control virus clearance, but an...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-20305-4

    authors： Lum FM,Couderc T,Chia BS,Ong RY,Her Z,Chow A,Leo YS,Kam YW,Rénia L,Lecuit M,Ng LFP

    更新日期：2018-01-30 00:00:00

  • Ecological responses to flow variation inform river dolphin conservation.

    abstract：:Many environmental flow (e-flow) studies and applications have predominantly used state-(i.e., at a single time point) and rate-(i.e., temporal change) based demographic characteristics of species representing lower trophic levels (e.g., fish communities) to build flow-ecology relationships, rather than using a proces...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-79532-3

    authors： Paudel S,Koprowski JL,Thakuri U,Sigdel R,Gautam RC

    更新日期：2020-12-18 00:00:00

  • Lithium and GADL1 regulate glycogen synthase kinase-3 activity to modulate KCTD12 expression.

    abstract：:Potassium channel tetramerization domain containing 12 (KCTD12), the auxiliary GABAB receptor subunit, is identified as a susceptibility gene for bipolar I (BPI) disorder in the Han Chinese population. Moreover, the single-nucleotide polymorphism (SNP) rs17026688 in glutamate decarboxylase-like protein 1 (GADL1) is sh...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-46655-1

    authors： Wu TN,Chen CK,Lee CS,Wu BJ,Sun HJ,Chang CH,Chen CY,Wu LS,Cheng AT

    更新日期：2019-07-16 00:00:00

  • Pharmacological therapies for infantile hemangiomas: A clinical study in 853 consecutive patients using a standard treatment algorithm.

    abstract：:Infantile hemangiomas are the most common infantile benign vascular tumor. While most infantile hemangiomas proliferate then involute, some may persist and require treatment for reasons including risk of disfigurement or functional impairment. Treatments currently include observation, pharmacological therapy, laser, c...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep21670

    authors： Zhang L,Yuan WE,Zheng JW

    更新日期：2016-02-15 00:00:00

  • Current prevalence of perioperative early venous thromboembolism and risk factors in Chinese adult patients with inguinal hernia (CHAT-1).

    abstract：:Venous thromboembolism (VTE) is an important postoperative complication. We investigated and analyzed the current inguinal hernia treatment methods and occurrence of early postoperative VTE in Chinese adults. This study involved data for patients with inguinal hernia hospitalized in 58 general hospitals in mainland Ch...

    journal_title：Scientific reports

    pub_type： 杂志文章,多中心研究

    doi：10.1038/s41598-020-69453-6

    authors： Wang M,Zhang G,Chen J,Li J,Che Y,Tang J,Li H,Li J,Ma Y

    更新日期：2020-07-29 00:00:00

  • Potential modulations in flatland: near-infrared sensitization of MoS2 phototransistors by a solvatochromic dye directly tethered to sulfur vacancies.

    abstract：:Near-infrared sensitization of monolayer MoS2 is here achieved via the covalent attachment of a novel heteroleptic nickel bis-dithiolene complex into sulfur vacancies in the MoS2 structure. Photocurrent action spectroscopy of the sensitized films reveals a discreet contribution from the sensitizer dye centred around 1...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-53186-2

    authors： Dalgleish S,Reissig L,Shuku Y,Ligorio G,Awaga K,List-Kratochvil EJW

    更新日期：2019-11-13 00:00:00

  • Efficient table-top dual-wavelength beamline for ultrafast transient absorption spectroscopy in the soft X-ray region.

    abstract：:We present a table-top beamline providing a soft X-ray supercontinuum extending up to 370 eV from high-order harmonic generation with sub-13 fs 1300 nm driving pulses and simultaneous production of sub-5 fs pulses centered at 800 nm. Optimization of high harmonic generation in a long and dense gas medium yields a phot...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-62461-6

    authors： Barreau L,Ross AD,Garg S,Kraus PM,Neumark DM,Leone SR

    更新日期：2020-04-01 00:00:00

  • The hydrogen sulfide metabolite trimethylsulfonium is found in human urine.

    abstract：:Hydrogen sulfide is the third and most recently discovered gaseous signaling molecule following nitric oxide and carbon monoxide, playing important roles both in normal physiological conditions and disease progression. The trimethylsulfonium ion (TMS) can result from successive methylation reactions of hydrogen sulfid...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep27038

    authors： Lajin B,Francesconi KA

    更新日期：2016-06-01 00:00:00

  • Active layers of high-performance lead zirconate titanate at temperatures compatible with silicon nano- and microeletronic [corrected] devices.

    abstract：:Applications of ferroelectric materials in modern microelectronics will be greatly encouraged if the thermal incompatibility between inorganic ferroelectrics and semiconductor devices is overcome. Here, solution-processable layers of the most commercial ferroelectric compound--morphotrophic phase boundary lead zircona...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep20143

    authors： Bretos I,Jiménez R,Tomczyk M,Rodríguez-Castellón E,Vilarinho PM,Calzada ML

    更新日期：2016-02-03 00:00:00

  • Fabrication of Ni-Ti-O nanotube arrays by anodization of NiTi alloy and their potential applications.

    abstract：:Nickel-titanium-oxide (Ni-Ti-O) nanotube arrays (NTAs) prepared on nearly equiatomic NiTi alloy shall have broad application potential such as for energy storage and biomedicine, but their precise structure control is a great challenge because of the high content of alloying element of Ni, a non-valve metal that canno...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep07547

    authors： Hang R,Liu Y,Zhao L,Gao A,Bai L,Huang X,Zhang X,Tang B,Chu PK

    更新日期：2014-12-18 00:00:00

  • Hepatitis C Virus Infection of Cultured Human Hepatoma Cells Causes Apoptosis and Pyroptosis in Both Infected and Bystander Cells.

    abstract：:Individuals infected with hepatitis C virus (HCV) are at high risk of developing progressive liver disease, including cirrhosis and hepatocellular carcinoma (HCC). How HCV infection causes liver destruction has been of significant interest for many years, and apoptosis has been proposed as one operative mechanism. In ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep37433

    authors： Kofahi HM,Taylor NG,Hirasawa K,Grant MD,Russell RS

    更新日期：2016-12-15 00:00:00

  • Promotion of a cancer-like phenotype, through chronic exposure to inflammatory cytokines and hypoxia in a bronchial epithelial cell line model.

    abstract：:Globally, lung cancer accounts for approximately 20% of all cancer related deaths. Five-year survival is poor and rates have remained unchanged for the past four decades. There is an urgent need to identify markers of lung carcinogenesis and new targets for therapy. Given the recent successes of immune modulators in c...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep18907

    authors： Baird AM,Gray SG,Richard DJ,O'Byrne KJ

    更新日期：2016-01-13 00:00:00

  • Innovative methods for random field establishment and statistical parameter inversion exemplified with 6082-T6 aluminum alloy.

    abstract：:This paper aims to eliminate the disharmony between simulation and experiment, and takes the mechanical properties of 6082-T6 Al alloy as an example. In order to obtain the equivalent distribution of material properties after considering the randomicity of materials, a new inversion method combining with stochastic fi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-54046-9

    authors： Zheng K,Yang K,Shi J,Yuan J,Zhou G

    更新日期：2019-11-28 00:00:00

  • Anti-Tumor Activity and Immunotherapeutic Potential of a Bisphosphonate Prodrug.

    abstract：:Bisphosphonates have benefits in breast cancer and multiple myeloma patients and have been used with adoptive immunotherapy with γδ T cells expressing Vγ2 Vδ2 TCRs. Although treatment with γδ T cells is safe, it has shown limited efficacy. Present bisphosphonates stimulate γδ T cells but were designed to inhibit bone ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-05553-0

    authors： Tanaka Y,Iwasaki M,Murata-Hirai K,Matsumoto K,Hayashi K,Okamura H,Sugie T,Minato N,Morita CT,Toi M

    更新日期：2017-07-20 00:00:00

  • Engineering a humanized telomerase reverse transcriptase gene in mouse embryonic stem cells.

    abstract：:Telomerase is expressed in adult mouse, but not in most human, tissues and mouse telomeres are much longer than those in humans. This interspecies difference of telomere homeostasis poses a challenge in modeling human diseases using laboratory mice. Using chromatinized bacterial artificial chromosome reporters, we dis...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-46160-5

    authors： Cheng,Zhao Y,Zhang F,Zhang J,Wang S,Zhu J

    更新日期：2019-07-04 00:00:00

  • Viscoelastic biomarker for differentiation of benign and malignant breast lesion in ultra- low frequency range.

    abstract：:Benign and malignant tumors differ in the viscoelastic properties of their cellular microenvironments and in their spatiotemporal response to very low frequency stimuli. These differences can introduce a unique viscoelastic biomarker in differentiation of benign and malignant tumors. This biomarker may reduce the numb...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-41885-9

    authors： Nabavizadeh A,Bayat M,Kumar V,Gregory A,Webb J,Alizad A,Fatemi M

    更新日期：2019-04-05 00:00:00

  • Role of innate immunity-triggered pathways in the pathogenesis of Sickle Cell Disease: a meta-analysis of gene expression studies.

    abstract：:Despite the detailed characterization of the inflammatory and endothelial changes observed in Sickle Cell Disease (SCD), the hierarchical relationship between elements involved in the pathogenesis of this complex disease is yet to be described. Meta-analyses of gene expression studies from public repositories represen...

    journal_title：Scientific reports

    pub_type： 杂志文章,meta分析

    doi：10.1038/srep17822

    authors： Hounkpe BW,Fiusa MM,Colella MP,da Costa LN,Benatti Rde O,Saad ST,Costa FF,dos Santos MN,De Paula EV

    更新日期：2015-12-09 00:00:00