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      Rosa1, a Transposable Element-Like Insertion, Produces Red Petal Coloration in Rose Through Altering RcMYB114 Transcription

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          Abstract

          Rose ( Rosa sp.) flowers have a rich diversity of colors resulting from the differential accumulation of anthocyanins, flavonols, and carotenoids. However, the genetic and molecular determinants of the red-petal trait in roses remains poorly understood. Here we report that a transposable element-like insertion (Rosa1) into RcMYB114, a R2R3-MYB transcription factor’s promoter region causes its transcription, resulting in red petals. In red-petal varieties, RcMYB114 is expressed specifically in flower organs, but is absent from non-red varieties. Sequencing, yeast two-hybrid, transient transformation, and promoter activity assays of RcMYB114 independently confirmed the role of Rosa1 in altering RcMYB114’s transcription and downstream effects on flower color. Genetic and molecular evidence confirmed that the Rosa1 transposable element-like insertion, which is a previously unknown DNA transposable element, is different from those in other plants and is a reliable molecular marker to screen red-petal roses.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

              The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                29 April 2022
                2022
                : 13
                : 857684
                Affiliations
                [1] 1Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences , Beijing, China
                [2] 2Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs , Beijing, China
                [3] 3Beijing Engineering Research Center of Functional Floriculture , Beijing, China
                [4] 4Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences , Beijing, China
                [5] 5Institute of Botany, University of Chinese Academy of Sciences , Beijing, China
                [6] 6Beijing Engineering Research Center for Deciduous Fruit Trees , Beijing, China
                Author notes

                Edited by: Jian Wu, China Agricultural University, China

                Reviewed by: Wenjun Huang, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS), China; Yaping Kou, Institute of Vegetables and Flowers (CAAS), China

                *Correspondence: Wanmei Jin, jwm0809@ 123456163.com

                This article was submitted to Plant Development and EvoDevo, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2022.857684
                9100400
                35574133
                7de6f2e7-4c18-437c-99a7-0ab85883613d
                Copyright © 2022 Li, Zhang, Yang, Wang, Xue, Fan, Sun, Zhang, Zhang and Jin.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 18 January 2022
                : 11 April 2022
                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 79, Pages: 13, Words: 8623
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                rosa1 transposable element-like,rcmyb114,transcription,petal color,rose,anthocyanin

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