Transcriptomics

We collected 529 RNA-seq samples from 40 BioProjects covering Ipomoea batatas and related species from NCBI SRA [1–10]. Samples span 16 tissue types and 21 experimental conditions across multiple cultivars. After quality trimming with Trimmomatic and alignment to reference genomes with HISAT2, expression levels were quantified as TPM and FPKM using StringTie. Samples were manually curated into 136 groups (tissue × condition combinations). Three main functions are provided: RNAseq Datasets, Gene Expression, and Co-expression.

RNAseq Datasets

A curated catalogue of 529 RNA-seq samples with full metadata: Run ID (linked to NCBI SRA), sample name, species, cultivar, tissue type, experimental condition, BioProject (linked to NCBI BioProject), journal, year, and DOI. The table is searchable and sortable. Interactive summary charts display sample distributions by species, year, tissue type, and experimental condition; clicking any chart slice filters the table accordingly.

Gene Expression

Query gene expression for any gene ID across 136 sample groups (16 tissues × 21 conditions) for three reference genomes:

IBA1.0 — 175,633 genes (I. batatas Xushu 18)
Beauregard_v4 — 270,428 genes (I. batatas Beauregard phased v4)
pasi3 — 42,750 genes (I. trifida NSP306 v3)

Expression is displayed as an interactive heatmap organized by condition (subplots) and tissue (columns) using Plotly.js. For groups with multiple replicates, representative cultivar values (Beauregard / Xushu 18 / Yanshu 25) are shown; otherwise the group median is used. Both TPM and FPKM units are supported.

Co-expression

Explore gene-centred co-expression neighborhoods for Xushu 18 (IBA1.0) and Beauregard (V4). Signed Pearson correlations are available from an absolute correlation threshold of 0.50. Users can select positive, negative, or both relationship types, adjust the minimum absolute correlation, inspect a radial network, review ranked neighbors, and download the filtered result as a TSV file.

PCA

Interactive principal component analysis of 419 RNA-seq samples for Beauregard v4, IBA1.0, and pasi3, computed independently for TPM and FPKM from the 5,000 most variable genes (log2(expression + 1)). Samples are colored by Plant Ontology superclass or anatomy term. Users can show or hide groups, search samples, zoom, download the plot as PNG, and export the visible samples as CSV. Coordinates are not comparable between datasets.

Data Processing

Raw reads were trimmed with Trimmomatic (v0.36; LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Clean reads were aligned to reference genomes using HISAT2 (v2.1.0) with default parameters. Gene expression levels were quantified using StringTie (v2.1.4).

References

[1]	Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements. Nat Methods, 2015, 12: 357–360.
[2]	Pertea M, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol, 2015, 33: 290–295.
[3]	Bolger A M, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30: 2114–2120.