https://doi.org/10.5061/dryad.qnk98sfs0

Description of the data and file structure

In "Small, but mitey: investigating the molecular genetic basis for mite domatia development and intraspecific variation in Vitis riparia using transcriptomics," we investigated the molecular genetic basis of mite domatia, structures on the underside of leaves that house mutualistic mites, and intraspecific variation in domatia size in Vitis riparia (riverbank grape). We preformed RNA-sequencing on domatia and control leaf tissue from two genotypes of V. riparia with distinct domatia sizes. We also collected and analyzed phenotypic data on domatia traits and leaf shape in these two genotypes. Here, we provide data from this manuscript and the link to the GitHub repository containing the code used for analyzing these data. The data provided includes i) the domatia phenotype data, ii) the domatia ontogeny data, iii) leaf scans accompanying the domatia ontogeny data (used for leaf landmarking analyses as well), and iv) the raw gene expression counts.

Files and variables

File: domatia_ontogeny_data.csv

Description: Domatia phenotype data across leaf development to characterize domatia ontogeny. Phenotypes were measured and scored from scanned leaves. Values with "NA" represent missing data.

Variables

• plant_code: Unique plant code
• genotype: Genotype
• plant: Plant number within genotype
• sequencing_id: ID of sample if used for sequencing
• leaf: Leaf ID
• density_1: Domatia hair density at vein axil 1 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_1: Radii of domatia at vein axil 1 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_2: Domatia hair density at vein axil 2 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_2: Radii of domatia at vein axil 2 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_3: Domatia hair density at vein axil 3 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_3: Radii of domatia at vein axil 3 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_4: Domatia hair density at vein axil 4 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_4: Radii of domatia at vein axil 4 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• notes: Additional notes if necessary (cells are empty if no unusual observations were noted during sampling)
• leaf_width: Width of leaf in centimeters

File: domatia_phenotypes.csv

Description:  Domatia phenotype data for both genotypes. Phenotypes were measured and scored from dried, pressed leaves. Values with "NA" represent missing data.

Variables

• plant_code: Unique plant code
• genotype: Genotype
• plant: Plant number within genotype
• sequencing_id: ID of sample if used for sequencing
• leaf: Leaf ID
• leaf_area (pixels): Area of leaf in pixels
• dry_mass (mg): Dry mass of leaf in milligrams
• density_1: Domatia hair density at vein axil 1 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_1: Radii of domatia at vein axil 1 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_2: Domatia hair density at vein axil 2 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_2: Radii of domatia at vein axil 2 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_3: Domatia hair density at vein axil 3 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_3: Radii of domatia at vein axil 3 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• density_4: Domatia hair density at vein axil 4 (see Graham et al., 2023 Figure 1A for exact vein axils on leaves) scores assigned using a nine-point scale where 0 represents no hair, and 9 represents a densely packed domatium with no leaf surface visible underneath
• radius_4: Radii of domatia at vein axil 4 in millimeters (see Graham et al., 2023 Figure 1A for exact vein axils on leaves)
• notes: Additional notes (cells are empty if no unusual observations were noted during sampling)

File: raw_reads_per_gene.zip

Description: A compressed folder containing raw reads per gene counts generated by mapping RNA reads to the V. riparia genome using STAR. The file names follow the same structure: "DOM-[sequencing_id][tissue type]ReadsPerGene.out.tab", with tissue type being "D" for domatia or "L" for control leaf tissue. Each individual file contains four tab-seperated columns (from left-to-right): 1)* V. riparia *gene ID, 2) counts for unstranded RNA-seq, 3) counts for the 1st read strand aligned with RNA (htseq-count option -s yes), 4) counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse). Each row contains raw read counts for the gene listed in column 1. These .tab files can be viewed using standard text editing software, including Windows Notepad, TextEdit (available on macOS), or Sublime Text. 

File: leaf_scans.zip

Description: A compressed folder containing the leaf scans used in this study to collect domatia ontogeny data and perform leaf landmarking analysis. The file names follow the same structure: "DOM-ONT-[genotype]-[plant].tif". These TIFF (.tif) files can be viewed using standard photo viewing software, including Windows Photo Viewer and Apple Preview.

Code/software

The code used to analyze the data as described in the manuscript is available on GitHub: https://github.com/eleanore-ritter/domatia-transcriptome

Access information

Other publicly accessible locations of the data:

• RNA sequencing data from this study are provided on the NCBI Sequence Read Archive under BioProject PRJNA1083535.