Data on occurrence of miRNA precursors in the Cucurbita maxima phloem sap

The phloem sieve elements (SEs), enucleate cells, contain RNAs, which are imported from surrounding tissues and cells, mostly companion cells tightly associated with SEs, and transported via the phloem over the whole plant body. The RNA phloem transport is essential for plant individual development and responses to environmental cues. Recently, we identified primary miRNA (pri-miRNA) sequences in de novo assembled transcriptome of Cucurbita maxima phloem sap and reported 11 most abundant pri-miRNAs [1]. Here, we provide the output of this analysis in complete detail. For the full set of pri-miRNAs identified in the C. maxima phloem sap transcriptome, data on relative abundance are provided along with annotated sequence data.


Data description
Sequence analysis of transcriptome sequencing data for Cucurbita maxima phloem sap revealed the presence of 35 contigs showing significant (e-value less than 1e-15) sequence similarity to known pri-miRNAs of Cucumis melo [1]; raw data on sequences of identified contigs are presented in Supplementary  Fig. S1. In a further analysis of the raw data, a relative abundance of each of these contigs in the phloem sap was characterized by the number of primary reads that could be aligned to this contig, read count normalized per 100 nucleotides of contig sequence, and average coverage (Table 1).
Specifications Table   Subject Plant Science Specific subject area miRNA-based regulation of gene expression in plants Type of data Table  How data were acquired Phloem transcriptome was assembled by SPAdes 3.12.0. Contigs containing miRNA precursors were identified by using BLAST. Alignments of primary reads with contigs were performed using Bowtie2. Data format Raw data, analyzed data Parameters for data collection Database search, dataset selection.

Description of data collection
Transcriptome sequencing data for C. maxima phloem sap were retrieved from NCBI Sequence Read Archive. Data source location The dataset is provided in Supplementary Fig. S1 Data accessibility With the article; raw data are provided in Supplementary Fig. S1, analyzed data are presented in Table 1

Value of the Data
This is the first report on the set of pri-miRNAs that are present in the phloem sap.
The reported data can be valuable for scientists studying cell-to-cell and phloem transport of RNA and, in general, molecular mechanisms of signalling in plants. These data will be useful for rational, knowledge-based selection of model pri-miRNAs for experimental analyses of molecular mechanism of pri-miRNA transport into SEs and long-distance trafficking via the phloem, as well as studies of phloem pri-miRNAs roles in regulation of gene expression.
maxima phloem sap transcriptome assembly included 96318 contigs. Sequences of C. melo pre-miRNAs annotated at miRBase [3] were downloaded in fasta format and used as queries for BLAST [4] searches for C. maxima assembled contigs containing related sequences. In order to obtain coverage values, primary reads were aligned with assembled contigs using Bowtie2 [5].
CRediT authorship contribution statement

Acknowledgments
This work was supported by the Russian Science Foundation (grant 17-14-01032).

Conflict of Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.