DOI: 10.5281/zenodo.10911533
title: Atypical epigenetic and small RNA control of transposons in clonally reproducing Spirodela polyrhiza.

description: The dataset contains all the original raw files for images, including protein and RNA blots, DNA and protein sequences used for phylogenetic trees, do plots…, and any other type of source data, sorted by figure and figure panel. Plasmids generated for this study have been deposited in Addgene. They are listed below together with previously existing plasmids obtained from Addgene. NGS data has been deposited on NCBI SRA, accession numbers of datasets used in each figure are listed accordingly in this document. Ready-to-visualize using IGV software files of all NGS datasets together with the S. polyrhiza 9509 gene and TE annotations are also provided.  The content of each file is:

 

FIGURE 1:

-        1b: Pictures of Spirodela polyrhiza.

 

FIGURE 3:

-        3a: Picture of Spirodela polyrhiza (used as well in S17a, S24b,d).

 

FIGURE 5:

-        5a: Western blot raw TIFF image files for the detection of H3K9me1, H3K9me2 and H3 in Arabidopsis and Spirodela.

 

FIGURE 7:

-        7a: Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in N. benthamiana.

-        7d: Raw scan image files of N. benthamiana leaves infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in N. benthamiana.

-        7e: Raw scan image files of Spirodela cultures in dishes infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in Spirodela.

 

SUPP FIGURE 1:

-        S1c: Picture of duckweed representatives from the five Lemnaceae genera individually or next to Arabidopsis for size comparison.

 

SUPP FIGURE 6:

-        Protein sequences, and their alignment, of several angiosperm DRB proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 7:

-        Protein sequences, and their alignment, of several angiosperm RDR proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 8:

-        Protein sequences, and their alignment, of several angiosperm DCL proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 9:

-        Protein sequences, and their alignment, of several angiosperm AGO proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 10:

-        DNA sequence of the Spirodela (Sp9509) Chromosome 7 fragment containing the AGO5 cluster.

 

SUPP FIGURE 11:

-        Protein sequences, and their alignment, of several angiosperm SHH proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 12:

-        Protein sequences, and their alignment, of several angiosperm Snf2 remodelers proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 13:

-        Protein sequences, and their alignment, of several angiosperm Class V SET-domain containing proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 14:

-        Protein sequences, and their alignment, of several angiosperm DNA methyltransferase proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 15:

-        Protein sequences, and their alignment, of several angiosperm RNA pol large subunit proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 16:

-        Protein sequences, and their alignment, of several angiosperm SPT5 and SPT5L proteins, including those identified in the S. polyrhiza 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPP FIGURE 17:

-        Picture of Arabidopsis (used as well in Fig. 3a, S24 a,c).

 

SUPP FIGURE 22:

-        S25c: Raw TIFF image files of the coomassie staining of histone acid-extraction protein samples run on SDS-PAGE gel.

-        S25d: Excel files with mass-spectrometry data used for quantification of histone modifications in Arabidopsis and Spirodela.

 

SUPP FIGURE 25:

-        S28a: Raw czi and TIFF image files of Arabidopsis interphase nuclei stained with DAPI.

-        S28b: Raw czi and TIFF image files of Spirodela interphase nuclei stained with DAPI.

 

SUPP FIGURE 30:

-        DNA sequence files (fasta) of TEs used to generate dot plots.

 

SUPP FIGURE 31:

-        DNA sequence files (fasta) of TEs used to generate dot plots.

 

SUPP FIGURE 32:

-        S35a: Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_gDNA in input and IP fractions from transient expression in N. benthamiana.

-        S35b: Intron-annotated genomic DNA sequences of AtAGO4 and SpAGO4a in GenBank (.gbk) format.

-        S35c: Raw image file of EtBr staining of agarose gel electrophoresis of 5’OH-RACE prior to gel excision and cloning.

-        S35d: Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in N. benthamiana.

 

SUPP FIGURE 33:

-        Pictures of Spirodela during pretreatment, manual and vacuum agroinfiltration and RUBY transient expression.

 

 

GENOME BROWSER TRACKS:

-        The following Integrative Genomics Viewer browser (https://igv.org) tracks are provided:

SPIRODELA

·       Spirodela 9509 genome (this study)

·       Spirodela gene annotations (V3.0)

·       Spirodela TE annotations (this study)

·       Spirodela H3K9me1 as log2[H3K9me1/H3] (this study)

·       Spirodela H3K9me2 as log2[H3K9me2/H3] (this study)

·       Spirodela H3K27me3 as log2[H3K27me3/H3] (this study)

·       Spirodela H3K4me3 as log2[H3K4me3/H3] (this study)

·       Spirodela TraPR purified 21-nt small RNAs (+ strand) (this study)

·       Spirodela TraPR purified 21-nt small RNAs (- strand) (this study)

·       Spirodela TraPR purified 22-nt small RNAs (+ strand) (this study)

·       Spirodela TraPR purified 22-nt small RNAs (- strand) (this study)

·       Spirodela TraPR purified 24-nt small RNAs (+ strand) (this study)

·       Spirodela TraPR purified 24-nt small RNAs (- strand) (this study)

·       Spirodela Illumina RNA seq coverage (this study)

·       Spirodela Illumina RNA seq reads (this study)

·       Spirodela PacBio Iso-seq coverage (this study)

·       Spirodela PacBio Iso-seq reads (this study)

 

ARABIDOPSIS

·       Arabidopsis Col-0 genome (TAIR10)

·       Arabidopsis gene annotations (TAIR10)

·       Arabidopsis TE annotations (TAIR10)

·       Arabidopsis seedlings H3K9me1 as log2[H3K9me1/H3] (this study)

·       Arabidopsis seedlings H3K9me2 as log2[H3K9me2/H3] (this study)

·       Arabidopsis seedlings H3K27me3 as log2[H3K27me3/H3] (this study)

·       Arabidopsis seedlings H3K4me3 as log2[H3K4me3/H3] (this study)

·       Arabidopsis seedlings TraPR purified 21-nt small RNAs (+ strand) (this study)

·       Arabidopsis seedlings TraPR purified 21-nt small RNAs (- strand) (this study)

·       Arabidopsis seedlings TraPR purified 22-nt small RNAs (+ strand) (this study)

·       Arabidopsis seedlings TraPR purified 22-nt small RNAs (- strand) (this study)

·       Arabidopsis seedlings TraPR purified 24-nt small RNAs (+ strand) (this study)

·       Arabidopsis seedlings TraPR purified 24-nt small RNAs (- strand) (this study)

 

NGS DATASETS:

 

All the NGS data generated for this study can be found under the SRA BioProject ID PRJNA1095698, Submission ID SUB14339214. The data was used to generate the following figure panels:

-        Figures: 1c-f, 2a-f, 3a-e, 4a-h, 5a-j, 6a-g, 7b, 7f-h

-        Supplementary Figures: S2, S3, S5a-c, S20a-b, S21a-c, S23a-b, S24a-f, S27a-d, S29, S30, S31, S32, S33, S34.

 

Publicly available sequencing data (from indicated datasets) was used to generate the following figures:

-        Figure 2a-f (Arabidopsis gene expression): GSM6892968

 

MASS SPECTROMETRY DATA:

 

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD050443. Data was used to generate:

-        Supplementary Figure 22d 

 

PLASMIDS:

 

The following plasmids generated in this study can be retrieved from Addgene under the following ID#:

-        p35S:FHA-AtAGO4_gDNA: #216838

-        p35S:FHA-SpAGO4a_gDNA: #216841

-        p35S::FHA-SpAGO4a_cDNA: #216842

 

The following plasmids used in this study were retrieved from Addgene under the following ID#:

-        p35S:RUBY: #160908

-        pZmUbq:RUBY: #160909

-        p35S:GFP-GUS: #167122

 

The following plasmids were a gift from Dr. Marco Incarbone (Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam 14476, Germany).

-        pAtUBQ:hpScarlet