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

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)本数据集包含该学术论文手稿的全部源数据与原始文件： 转座子扩张与形态学极简被子植物巴西无根萍（Wolffia brasiliensis）的小RNA与DNA甲基化组重编程相关联 作者：Daniel Buendía-Ávila¹,², Verónica Barragán-Borrero¹, Pablo Luna-Rodriguez¹, Mary Akinyuwa¹, Laura Morello³ 及 Arturo Marí-Ordóñez¹*。 本数据集包含论文中使用的全部原始数据、巴西无根萍7522克隆的参考基因组及其注释文件，以及适用于所有下一代测序（Next-Generation Sequencing, NGS）数据集的即用型基因组浏览器轨道文件。原始NGS数据已提交至美国国家生物技术信息中心序列读取档案（NCBI SRA），各图所用数据集的登录号已在本文档中对应列出。各文件内容如下： ### 图1 - 1a：不同浮萍物种的照片：多根紫背浮萍（Spirodela polyrhiza #7656）、斑点无根萍（Landoltia punctata #7487）、小浮萍（Lemna minor #8623）、剑形沃尔夫浮萍（Wolffiella gladiata #8768）、巴西无根萍（Wolffia brasiliensis #7522）及无根萍（Wolffia arrhizal #7193）。 - 1b：用于估算巴西无根萍基因组大小的流式细胞术文件（.fcs格式）。本文档同时提供补充图S1中所用的无根萍（W. arrhizal）数据。 - 1c：巴西无根萍#7522经4',6-二脒基-2-苯基吲哚（DAPI）染色的有丝分裂中期相图像文件。 ### 图4 - 4a：参见补充图S14b - 4d：参见补充图S15a - 4e：瞬时表达增强绿色荧光蛋白（eGFP）的巴西无根萍特写照片。 ### 图5 - 5b：巴西无根萍反向重复序列的DNA序列，格式为fasta（.fa）。该序列亦用于补充实验S17。 ### 图6 - 6a：巴西无根萍照片。该图像文件亦用于补充图S2a。 ### 补充图S1 - 参见图1b。 ### 补充图S2 - S2a：巴西无根萍照片，亦用于图6a。 - S2b：用于描述巴西无根萍形态与营养生长的照片。 ### 补充图S7 - S7a：巴西无根萍与多根紫背浮萍的DCL蛋白序列及其比对结果，包含从巴西无根萍7522克隆基因组中鉴定得到的序列，用于构建序列两两比对，格式为fasta（.fa）。 ### 补充图S8 - S8b：用于生成点图的巴西无根萍WbDCL1a/b基因组位点的DNA序列，格式为fasta（.fa）。 ### 补充图S9 - 多种被子植物DCL蛋白的序列及其比对结果，包含从巴西无根萍7522克隆基因组中鉴定得到的序列，用于构建系统发育树，格式为fasta（.fa）。同时提供Nexus格式（.nxs）的机器可读树文件。 ### 补充图S10 - S10c：多种被子植物DCL蛋白的序列及其比对结果，包含从多根紫背浮萍9509基因组中鉴定得到的序列，用于构建系统发育树，格式为fasta（.fa）。同时提供Nexus格式（.nxs）的机器可读树文件。 - S10d：JBrowse 2基因组浏览器截图（详见基因组浏览器轨道文件）。 ### 补充图S14 - S14a：巴西无根萍miR390的DNA序列，格式为fasta（.fa）。 - S14b：鉴定得到的两个巴西无根萍TAS3位点的DNA序列。 ### 补充图S15 - S15a-b：不同时间点的巴西无根萍照片，展示农杆菌浸润后ZmUBQ:eGFP的表达情况。提供各时间点的感兴趣区域（Region of Interest, ROI）、已鉴定并定量的无根萍样本、定量结果与分析数据。 ### 补充图S18 - 用于生成点图的包含簇的巴西无根萍反向重复序列的DNA序列，格式为fasta（.fa）。 ### 补充图S23 - S23a-d：JBrowse 2基因组浏览器截图（详见基因组浏览器轨道文件）。 ### 补充图S24 - JBrowse 2基因组浏览器截图（详见基因组浏览器轨道文件）。 ### 补充图S26 - S23a-c：JBrowse 2基因组浏览器截图（详见基因组浏览器轨道文件）。 --- ### 基因组轨道文件（GENOME TRACKS） 本数据集提供以下基因组浏览器轨道： #### 基因组与序列文件 · 巴西无根萍7522基因组序列 · 巴西无根萍7522 mRNA序列 · 巴西无根萍7522 CDS序列 · 巴西无根萍7522蛋白质序列 #### 基因组浏览器轨道 · 巴西无根萍7522 >100bp转座因子（Transposable Element, TE）注释 · 巴西无根萍7522重复序列注释 · 巴西无根萍7522基因注释 · 巴西无根萍7522 IR+簇注释 · 巴西无根萍7522 TraPR纯化的21-nt小RNA标准化覆盖度（正链） · 巴西无根萍7522 TraPR纯化的21-nt小RNA标准化覆盖度（负链） · 巴西无根萍7522 TraPR纯化的22-nt小RNA标准化覆盖度（正链） · 巴西无根萍7522 TraPR纯化的22-nt小RNA标准化覆盖度（负链） · 巴西无根萍7522 TraPR纯化的24-nt小RNA标准化覆盖度（正链） · 巴西无根萍7522 TraPR纯化的24-nt小RNA标准化覆盖度（负链） · 巴西无根萍7522 Illumina RNA测序覆盖度 · 巴西无根萍7522 PacBio Iso-seq聚类读数 --- ### NGS数据集（NGS DATASETS） 本研究产生的全部NGS数据可在SRA生物项目编号PRJNA1405057下获取。该数据用于生成以下图表组： - 主图：1a、2a-h、3a-g、4a-c、f-h、5a、d-k、6a-e、7a-f、8a-i - 补充图：S3、S4、S5、S8a、S10d、S11、S12、S13、S14、S16、S17、S18、S19、S20、S21、S22、S23、S24、S25、S26、S27。 公开可用的测序数据（来自指定数据集）用于生成以下图表： - 图3d（多根紫背浮萍基因表达数据：SRX26200034-36） - 图6b（多根紫背浮萍酶学甲基化测序（Enzymatic Methyl-sequencing, EM-seq）数据：SRR30812844-46） - 补充图S11（拟南芥基因表达数据：GSM6892967-69；多根紫背浮萍数据：参见图3） --- ### 质粒（PLASMIDS） 本研究中使用的以下质粒获取自以下途径： - pZmUbq:eGFP：欧洲质粒库（European Plasmid Repository）#869 - pGGSun-pUBIPars-hpScarlet 由Marco Incarbone博士（德国波茨坦科学园马克斯·普朗克分子植物生理学研究所，波茨坦14476）惠赠。