DOI: 10.5281/zenodo.18759226
title: Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis

description: The dataset contains all the source data and original raw files for the manuscript: 

 

Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis

 

Daniel Buendía-Ávila1,2, Verónica Barragán-Borrero1, Pablo Luna-Rodriguez1, Mary Akinyuwa1, Laura Morello3 and Arturo Marí-Ordóñez1*.

 

The dataset contains all the raw data used in the manuscript and the W. brasiliensis genome and its annotations as well as ready-to-use genome browser tracks for all the NGS datasets. Raw NGS data has been deposited on NCBI SRA, accession numbers of datasets used in each figure are listed accordingly in this document.  The content of each file is:

 

FIGURE 1:

-        1a: Picture of different duckweed species: Spirodela polyrhiza #7656, Landoltia punctata #7487, Lemna minor #8623, Wolffiella gladiata #8768, Wolffia brasiliensis #7522 and Wolffia arrhizal #7193. 

-        1b: Flow cytometry files (.fcs) used for genome size estimation of Wolffia brasiliensis. Data from W.arrhiza in figure S1 is also provided here

-        1c: Image file of Wolffia brasiliensis #7522 DAPI stained mitotic metaphase.

 

FIGURE 4:

-        4a: See Figure S14b

-        4d: See Figure S15a

-        4e: Close pictures of Wolffia brasiliensis transiently expressing eGFP 

 

FIGURE 5

-        5b: DNA Sequence of the Wolffia brasiliensis Inverted Repeat, in fasta (.fa) format. This sequence was also used in S17

 

FIGURE 6:

-        6a: Image of a Wolffia brasiliensis. Image file was also used in S2a 

 

FIGURE S1:

-        See Figure 1b.

 

FIGURE S2:

-        S2a: Image of Wolffia brasiliensis also used in Figure 6a.

-        S2b: Images of Wolffia brasiliensis used to describe morphology and vegetative growth.

 

FIGURE S7:

-        S7a: Protein sequences, and their alignment, of Wolffia brasiliensis and Spirodela polyrhiza DCL proteins, including those identified in the W. brasiliensis clone 7522 genome used to build the sequence pair-wise comparison in fasta (.fa) format. 

 

FIGURE S8:

-        S8b:DNA Sequence of the WbDCL1a/b genomic loci used to generate the dot plot in fasta (.fa) format. 

 

FIGURE S9:

-        Protein sequences, and their alignment, of several angiosperm DCL proteins, including those identified in the W.brasiliensis clone 7522 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).

 

SUPPLEMENTAL FIGURE S10:

 

-        S10c: 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).

-        S10d: JBrowse 2 genome browser screenshot (see genome browser track files)

 

SUPPLEMENTAL FIGURE S14:

-        S14a: DNA Sequence of the Wolffia brasiliensis miR390 in fasta (.fa) format.

-        S14b: DNA Sequence of the two Wolffia brasiliensis identified TAS3 loci.

 

SUPPLEMENTAL FIGURE S15:

-        S15a-b: Pictures of different timepoints from Wolffia brasiliensis showing expression of ZmUBQ:eGFP after Agrobacteriuminfiltration. ROIs (identified and quantified Wolffias are provided for each timepoint), quantification and analysis.

 

SUPPLEMENTAL FIGURE S18:

-        DNA Sequence of the Wolffia brasiliensis Inverted Repeat containing clusters used for the dot plot in fasta (.fa) format.

 

SUPPLEMENTAL FIGURE S23:

-        S23a-d: JBrowse 2 genome browser screenshot (see genome browser track files)

 

SUPPLEMENTAL FIGURE S24:

-        JBrowse 2 genome browser screenshot (see genome browser track files)

 

SUPPLEMENTAL FIGURE S26:

-        S23a-c: JBrowse 2 genome browser screenshot (see genome browser track files)

  

GENOME TRACKS

-        The following Genome Browser tracks are provided:

Genome and CDS, mRNA and Protein sequences

·       Wolffia brasiliensis 7522 genome

·       Wolffia brasiliensis 7522 mRNA sequences

·       Wolffia brasiliensis 7522 CDS sequences

·       Wolffia brasiliensis 7522 protein sequences

Genome browser tracks

·       Wolffia brasiliensis 7522 TE annotations >100bp

·       Wolffia brasiliensis 7522 Repeat annotations

·       Wolffia brasiliensis 7522 gene annotations

·       Wolffia brasiliensis 7522 IR+ cluster annotations

 

·       Wolffia brasiliensis 7522 TraPR purified 21-nt small RNAs normalized coverage (+ strand)

·       Wolffia brasiliensis 7522 TraPR purified 21-nt small RNAs normalized coverage (- strand)

·       Wolffia brasiliensis 7522 TraPR purified 22-nt small RNAs normalized coverage (+ strand)

·       Wolffia brasiliensis 7522 TraPR purified 22-nt small RNAs normalized coverage (- strand)

·       Wolffia brasiliensis 7522 TraPR purified 24-nt small RNAs normalized coverage (+ strand)

·       Wolffia brasiliensis 7522 TraPR purified 24-nt small RNAs normalized coverage (- strand)

·       Wolffia brasiliensis 7522 Illumina RNA seq coverage   

·       Wolffia brasiliensis 7522 PacBio Iso-seq clustered reads

 

NGS DATASETS:

 

All the NGS data generated for this study can be found under the SRA BioProject ID PRJNA1405057.  The data was used to generate the following figure panels:

-        Figures: 1a, 2a-h, 3a-g, 4a-c,f-h, 5a,d-k, 6a-e, 7a-f, 8a-i

-        Supplemental Figures: S3, S4, S5, S8a S10d, S11, S12, S13, S14, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27.

 

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

-        Figure 3d (Spirodela gene expression SRX26200034-36)

-        Figure 6b (Spirodela EM-seq SRR30812844-46)

-        Figure S11, (Arabidopsis gene expression: GSM6892967-69, Spirodela: See Figure 3)

 

PLASMIDS:

The following plasmids used in this study were retrieved from following:

-        pZmUbq:eGFP: European Plasmid Repostiory #869

-        pGGSun-pUBIPars-hpScarlet was a gift from Dr. Marco Incarbone (Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam 14476, Germany)