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      Cold-Triggered Induction of ROS- and Raffinose Metabolism in Freezing-Sensitive Taproot Tissue of Sugar Beet

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          Abstract

          Sugar beet ( Beta vulgaris subsp. vulgaris) is the exclusive source of sugar in the form of sucrose in temperate climate zones. Sugar beet is grown there as an annual crop from spring to autumn because of the damaging effect of freezing temperatures to taproot tissue. A collection of hybrid and non-hybrid sugar beet cultivars was tested for winter survival rates and freezing tolerance. Three genotypes with either low or high winter survival rates were selected for detailed study of their response to frost. These genotypes differed in the severity of frost injury in a defined inner region in the upper part of the taproot, the so-called pith. We aimed to elucidate genotype- and tissue-dependent molecular processes during freezing and combined analyses of sugar beet anatomy and physiology with transcriptomic and metabolite profiles of leaf and taproot tissues at low temperatures. Freezing temperatures induced strong downregulation of photosynthesis in leaves, generation of reactive oxygen species (ROS), and ROS-related gene expression in taproots. Simultaneously, expression of genes involved in raffinose metabolism, as well as concentrations of raffinose and its intermediates, increased markedly in both leaf and taproot tissue at low temperatures. The accumulation of raffinose in the pith tissue correlated with freezing tolerance of the three genotypes. We discuss a protective role for raffinose and its precursors against freezing damage of sugar beet taproot tissue.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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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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                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
                03 September 2021
                2021
                : 12
                : 715767
                Affiliations
                [1] 1Department of Plant Physiology, University of Kaiserslautern , Kaiserslautern, Germany
                [2] 2Department of Biochemistry, FAU Erlangen-Nürnberg , Erlangen, Germany
                [3] 3CRDS, Südzucker AG , Obrigheim/Pfalz, Germany
                [4] 4KWS SAAT SE & Co. KGaA , Einbeck, Germany
                Author notes

                Edited by: Dean E. Riechers, University of Illinois at Urbana-Champaign, United States

                Reviewed by: Charles L. Guy, University of Florida, United States; Bishal Tamang, University of Illinois at Urbana-Champaign, United States; Ravindra N. Chibbar, University of Saskatchewan, Canada

                *Correspondence: Benjamin Pommerrenig, pommerre@ 123456bio.uni-kl.de

                This article was submitted to Plant Abiotic Stress, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2021.715767
                8446674
                34539707
                f20d1848-5871-415d-819f-2d81c98127ee
                Copyright © 2021 Keller, Müdsam, Rodrigues, Kischka, Zierer, Sonnewald, Harms, Czarnecki, Fiedler-Wiechers, Koch, Neuhaus, Ludewig and Pommerrenig.

                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
                : 27 May 2021
                : 10 August 2021
                Page count
                Figures: 7, Tables: 1, Equations: 0, References: 89, Pages: 19, Words: 13295
                Funding
                Funded by: Federal Ministry of Education and Research 10.13039/501100002347
                Award ID: FKZ 031B0185
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                sugar beet,freezing,pith,reactive oxygen species,raffinose
                Plant science & Botany
                sugar beet, freezing, pith, reactive oxygen species, raffinose

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