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      The Role of Auxin in the Pattern Formation of the Asteraceae Flower Head (Capitulum) 1

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          Abstract

          Auxin and key flower meristem genes play a pivotal role in patterning of the capitulum, a key innovation that taxonomically defines the daisy family.

          Abstract

          Nature often creates complex structures by rearranging pre-existing units. One such example is the flower head (capitulum) in daisies, where a group of flowers (florets) and phyllaries (modified bracts) are arranged to superficially mimic a single flower. The capitulum is a key taxonomical innovation that defines the daisy family (Asteraceae), the largest flowering plant group. However, patterning mechanisms underlying its structure remain elusive. Here, we show that auxin, a plant hormone, provides a developmental patterning cue for the capitulum. During capitulum development, a temporal auxin gradient occurs, regulating the successive and centripetal formation of distinct florets and phyllaries. Disruption of the endogenous auxin gradient led to homeotic conversions of florets and phyllaries in the capitulum. Furthermore, auxin regulates floral meristem identity genes, such as Matricaria inodora RAY2 and M. inodora LEAFY, which determine floret and phyllary identity. This study reveals the mechanism of capitulum patterning and highlights how common developmental tools, such as hormone gradients, have independently evolved in plants and animals.

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          Analyzing real-time PCR data by the comparative C(T) method.

          Two different methods of presenting quantitative gene expression exist: absolute and relative quantification. Absolute quantification calculates the copy number of the gene usually by relating the PCR signal to a standard curve. Relative gene expression presents the data of the gene of interest relative to some calibrator or internal control gene. A widely used method to present relative gene expression is the comparative C(T) method also referred to as the 2 (-DeltaDeltaC(T)) method. This protocol provides an overview of the comparative C(T) method for quantitative gene expression studies. Also presented here are various examples to present quantitative gene expression data using this method.
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            Primer3Plus, an enhanced web interface to Primer3

            Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible options. This makes the interface powerful, but at the same time confusing for occasional users. Primer3Plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. It focuses on the task at hand, and hides detailed settings from the user until these are needed. We also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can be sent to an order form, allowing tight integration into laboratory ordering systems. Moreover, the open architecture of Primer3Plus allows easy expansion or integration of external software packages. The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus.
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              A rapid bootstrap algorithm for the RAxML Web servers.

              Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources.
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                Author and article information

                Journal
                Plant Physiol
                Plant Physiol
                plantphysiol
                aspb
                Plant Physiology
                American Society of Plant Biologists
                0032-0889
                1532-2548
                February 2019
                20 November 2018
                20 November 2018
                : 179
                : 2
                : 391-401
                Affiliations
                [1]Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT UK
                Author notes
                [2]

                Current address: Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN UK.

                [3]

                These authors contributed equally to this work.

                [4]

                Present address: Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, California 92093.

                [5 ]Author for contact: minsung.kim@ 123456manchester.ac.uk .
                [6]

                Senior author.

                The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors ( www.plantphysiol.org) is: Minsung Kim ( minsung.kim@ 123456manchester.ac.uk ).

                M.K. conceived the project and designed the experiments; N.Z., S.H.C.D., H.G., and V.S. designed and conducted the experiments; M.K. and N.Z. drafted the manuscript; all authors edited the manuscript.

                Author information
                http://orcid.org/0000-0002-2505-2734
                http://orcid.org/0000-0003-4717-000X
                http://orcid.org/0000-0002-3703-7531
                http://orcid.org/0000-0002-9930-1377
                http://orcid.org/0000-0002-8470-793X
                Article
                201801119R1
                10.1104/pp.18.01119
                6426414
                30459264
                42b0f4c1-e7f5-454b-9603-01dbca5decc7
                © 2019 The author(s). All Rights Reserved.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 September 2018
                : 13 November 2018
                Page count
                Figures: 4, Tables: 0, Equations: 0, References: 60, Pages: 11
                Funding
                Funded by: Biotechnology and Biological Sciences Research Council
                Funded by: BBSRC
                Award ID: BB/I012982/1
                Funded by: Royal Society
                Award ID: RG 2009/R1
                Funded by: BBSRC DTP
                Award ID: BB/F017227/1
                Award ID: BB/J014478/1
                Categories
                Research Reports
                Custom metadata
                v1

                Plant science & Botany
                Plant science & Botany

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