Supporting information for: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development
Creators: name: Bačovský, Václav
name: Čegan, Radim
name: Tihlaříková, Eva
name: Neděla, Vilém
name: Hudzieczek, Vojtěch
name: Smrža, Lubomír
name: Janíček, Tomáš
name: Beneš, Vladimír
name: Hobza, Roman
Publisher: name: Zenodo
Year: 2021

description: This collection of supplementary data include raw RNA-seq data for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites), 12 Supplementary figures, 5 Supplementary Tables, 8 Datasets and. RNA-seq data were not processed. The supplementary figures and tables support major findings of the main article titled "<b>Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development" </b>and include schematic workflow of the experimental procedure regarding <i>in vitro </i>assay, phenotyping and bioinformatic analysis. Further collection of figures includes a pedigree of androhermahroditic inheritance, the effect of chemical treatment on developing seedlings, electron micrographs of female flower in the androhermaphrodite progeny, viability staining, carpel examination, RNA-seq data validation, Volcano plots, TEs expression, gene ontology and clustering analysis. Tables include data for transcriptomic analysis. Supplemental Datasets consist of data for each analysis in the article, genes ID, identified DEGs, repeat expression analysis, described GO terms, ID for clustering analysis, genes identified by Venn diagrams and genes related to flower development.
description: Please, find the "ReadMe" file. Note that there are no missing values. Funding provided by: Grantová Agentura České Republiky<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001824<br>Award Number: 19-02476YFunding provided by: Grantová Agentura České Republiky<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001824<br>Award Number: 19-03909SFunding provided by: e-Infrastruktura CZ*<br>Crossref Funder Registry ID: <br>Award Number: LM2018140
description: <strong>RNA isolation, image capturing and bioinformatic analysis</strong> RNA was isolated in biological triplicates from <em>Silene latifolia </em>flowers of stage 11 based on Zluvova <i>et. al</i>. (2007; Note S1). Transcriptome sequencing libraries were prepared from total RNA with the Illumina TruSeq mRNA Library Prep Kit at the Genomics Core Facility (Genecore, EMBL, Heidelberg). The sequencing of the libraries was conducted at the Genecore on Illumina NextSeq500 instrument with 75-bp paired-end reads. The quality of sequencing reads was inspected in FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastq). All R scripts were run in R studio, and all software and tools used are listed in supplementary notes (Note S3). For phenotyping, flowers were opened with dissecting needles, and petals and sepals were carefully removed for final imaging and ovule and placenta examination (Note S2). A pollen staining protocol Peterson <em>et al</em>. (2010) was followed. For morphological characterization of flowers in their fresh state free of any microstructural changes or artifacts, a field emission environmental scanning electron microscope equipped for advanced control of thermodynamic conditions inside the specimen chamber (Neděla <i>et al.</i>, 2020), the wide field aperture detector (WFAD) for ESEM (newly developed for the purpose of this research at the ISI ASCR), and the ionization secondary electron detector with an electrostatic separator (ISEDS) were used (Neděla <i>et al.</i>, 2018). For statistical analysis, one-way ANOVA followed by Tukey's multiple comparisons test for Pollen viability and ovule number was performed using GraphPad Prism version 8.0.0 for Windows, GraphPad Software, San Diego, California USA (www.graphpad.com). Putative sex-linked transcripts were identified in the <i>S. latifolia </i>reference transcriptome (Zemp <i>et al.</i>, 2016) by blast-n searches against previously published sets of sex-linked transcripts (Bergero &amp; Charlesworth, 2011; Chibalina &amp; Filatov, 2011; Muyle <i>et al.</i>, 2012; Papadopulos <i>et al.</i>, 2015; Zemp <i>et al.</i>, 2016). For blast searches, blast-n with e-value 1E–40 from blast-all 2.2.26 was used (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/). As sex-linked transcripts we considered those with at least one hit against mentioned datasets (Table S2). <strong>References</strong> Bergero R, Charlesworth D. 2011. Preservation of the Y Transcriptome in a 10-Million-Year-Old Plant Sex Chromosome System. <i>Current Biology</i> 21: 1470–1474. Chibalina MV, Filatov DA. 2011. Plant Y Chromosome Degeneration Is Retarded by Haploid Purifying Selection. <i>Current Biology</i> 21: 1475–1479. Muyle A, Zemp N, Deschamps C, Mousset S, Widmer A, Marais GAB. 2012. Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes. <i>PLoS Biology</i> 10: 1–8. Neděla V, Tihlaříková E, Maxa J, Imrichová K, Bučko M, Gemeiner P. 2020. Simulation-based optimisation of thermodynamic conditions in the ESEM for dynamical in-situ study of spherical polyelectrolyte complex particles in their native state. <i>Ultramicroscopy</i> 211: 112954. Neděla V, Tihlaříková E, Runštuk J, Hudec J. 2018. High-efficiency detector of secondary and backscattered electrons for low-dose imaging in the ESEM. <i>Ultramicroscopy</i> 184: 1–11. Papadopulos AST, Chester M, Ridout K, Filatov DA. 2015. Rapid Y degeneration and dosage compensation in plant sex chromosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i> 112: 13021–13026. Peterson R, Slovin JP, Chen C. 2010. A simplified method for differential staining of aborted and non-aborted pollen grains. <i>International Journal of Plant Biology</i> 1: 13. Zemp N, Tavares R, Muyle A, Charlesworth D, Marais GAB, Widmer A. 2016. Evolution of sex-biased gene expression in a dioecious plant. <i>Nature plants</i> 2: 16168. Zluvova J, Zak J, Janousek B, Vyskot B. 2010. Dioecious Silene latifolia plants show sexual dimorphism in the vegetative stage. <i>BMC plant biology</i> 10: 208.