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      Nutritional and tissue-specific regulation of cytochrome P450 CYP711A MAX1 homologues and strigolactone biosynthesis in wheat

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          Abstract

          Strigolactones (SLs) are a class of phytohormones regulating branching/tillering, and their biosynthesis has been associated with nutritional signals and plant adaptation to nutrient-limiting conditions. The enzymes in the SL biosynthetic pathway downstream of carlactone are of interest as they are responsible for structural diversity in SLs, particularly cytochrome P450 CYP711A subfamily members, such as MORE AXILLARY GROWTH1 ( MAX1) in Arabidopsis. We identified 13 MAX1 homologues in wheat, clustering in four clades and five homoeologous subgroups. The utilization of RNA-sequencing data revealed a distinct expression pattern of MAX1 homologues in above- and below-ground tissues, providing insights into the distinct roles of MAX1 homologues in wheat. In addition, a transcriptional analysis showed that SL biosynthetic genes were systematically regulated by nitrogen supply. Nitrogen limitation led to larger transcriptional changes in the basal nodes than phosphorus limitation, which was consistent with the observed tillering suppression, as wheat showed higher sensitivity to nitrogen. The opposite was observed in roots, with phosphorus limitation leading to stronger induction of most SL biosynthetic genes compared with nitrogen limitation. The observed tissue-specific regulation of SL biosynthetic genes in response to nutritional signals is likely to reflect the dual role of SLs as rhizosphere signals and branching inhibitors.

          Abstract

          Expression analysis of strigolactone biosynthetic genes revealed tissue-specific responsiveness to nutritional signals and distinct spatial expression patterns of MAX1genes in Triticum aestivum.

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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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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                J Exp Bot
                J Exp Bot
                exbotj
                Journal of Experimental Botany
                Oxford University Press (UK )
                0022-0957
                1460-2431
                28 March 2023
                10 January 2023
                10 January 2023
                : 74
                : 6
                : 1890-1910
                Affiliations
                Rothamsted Research , West Common, Harpenden AL5 2JQ, UK
                Rothamsted Research , West Common, Harpenden AL5 2JQ, UK
                Rothamsted Research , West Common, Harpenden AL5 2JQ, UK
                Laboratoire de Physico-Chimie et Bioanalytique, Centre Mondial de l’Innovation Roullier, Timac Agro International , 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
                Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation Roullier, Timac Agro International , 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
                Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation Roullier, Timac Agro International , 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
                Plant and Crop Sciences, School of Biosciences, University of Nottingham , Sutton Bonington Campus, Loughborough LE12 5RD, UK
                Rothamsted Research , West Common, Harpenden AL5 2JQ, UK
                CIMMYT , Mexico
                Author notes
                Author information
                https://orcid.org/0000-0001-7069-363X
                Article
                erad008
                10.1093/jxb/erad008
                10049918
                36626359
                9d229e93-6f02-46d5-80c6-002fe74239d3
                © The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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

                History
                : 18 August 2022
                : 05 January 2023
                : 09 January 2023
                : 16 February 2023
                Page count
                Pages: 21
                Funding
                Funded by: Centre Mondial de l’Innovation Roullier, DOI 10.13039/501100010063;
                Funded by: University of Nottingham, DOI 10.13039/501100000837;
                Funded by: Rothamsted Research, DOI 10.13039/100010273;
                Funded by: Biotechnology and Biological Sciences Research Council, DOI 10.13039/501100000268;
                Award ID: BB/P016855/1
                Categories
                Research Papers
                Growth and Development
                AcademicSubjects/SCI01210

                Plant science & Botany
                cytochrome p450 cyp711a,gene expression,max1,nitrogen,strigolactones,tillering,wheat (triticum aestivum)

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