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      The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

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          SUMMARY

          Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early‐diverging angiosperms that have gone through woodiness–herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales. By considering differentially expressed genes, we identified candidate genes that are involved in the morphogenesis of the white leaves in S. chinensis. Among those genes, we verified – in a transgenic experiment with Arabidopsis – that increasing the expression of the “pseudo‐etiolation in light” gene ( ScPEL) can inhibit the biosynthesis of chlorophyll. ScPEL is thus likely responsible for the switches between green and white leaves, suggesting that changes in gene expression may underlie the evolution of pollination strategies. Despite being an herbaceous plant, S. chinensis still has vascular cambium and maintains the potential for secondary growth as a woody plant, because the necessary machinery, i.e., the entire gene set involved in lignin biosynthesis, is well preserved. However, similar expression levels of two key genes (CCR and CAD) between the stem and other tissues in the lignin biosynthesis pathway are possibly associated with the herbaceous nature of S. chinensis. In conclusion, the S. chinensis genome provides valuable insights into the adaptive evolution of pollination in Saururaceae and reveals a possible mechanism for the evolution of herbaceousness in magnoliids.

          Significance Statement

          The Saururus chinensis genome provides an important new resource for the understanding of the “rapid radiation” of early angiosperms, coined by Darwin as an “abominable mystery,” and recovered a sister relationship for magnoliids and Chloranthales. Experiments and bioinformatics analyses reveal the molecular mechanism for the pollination‐related organ morphogenesis (white leaves during flowering time) in S. chinensis and an adaptive evolution of pollination strategy in Saururaceae, and provide valuable insights into the woodiness–herbaceousness transition in magnoliids.

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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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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              Fast gapped-read alignment with Bowtie 2.

              As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                The Plant Journal
                The Plant Journal
                Wiley
                0960-7412
                1365-313X
                March 2023
                February 09 2023
                March 2023
                : 113
                : 5
                : 1021-1034
                Affiliations
                [1 ] College of Horticulture, Academy for Advanced Interdisciplinary Studies Nanjing Agricultural University Nanjing 210095 China
                [2 ] Center for Plant Diversity and Systematics, Institute of Botany Jiangsu Province and Chinese Academy of Sciences Nanjing 210014 China
                [3 ] Department of Plant Biotechnology and Bioinformatics Ghent University, VIB‐UGent Center for Plant Systems Biology B‐9052 Belgium
                [4 ] State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture Northwest A&F University Yangling 712100 China
                [5 ] Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 China
                [6 ] Max Planck Institute of Molecular Plant Physiology Potsdam Science Park Am Mühlenberg 1 Potsdam 14476 Germany
                [7 ] Fairy Lake Botanical Garden Shenzhen & Chinese Academy of Sciences Shenzhen 518004 Guangdong China
                [8 ] State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences Nanjing University Nanjing 210023 China
                [9 ] Department of Biochemistry, Genetics and Microbiology University of Pretoria Pretoria 0028 South Africa
                Article
                10.1111/tpj.16097
                7614262
                36602036
                6e7dfb3f-6eca-44c1-9ca6-c9687265f571
                © 2023

                http://creativecommons.org/licenses/by-nc-nd/4.0/

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