Processed transcriptomic data supporting comparative analysis of apple rootstock responses and loquat vigor

This dataset contains processed transcriptomic data and reproducibility resources supporting the study "Comparative Transcriptomics of Apple Rootstock Responses Identifies Candidate Genes for Loquat Vigor." The archive includes Salmon quantification results for 51 publicly available RNA-seq runs, differential-expression results from apple rootstock comparisons, apple-centered cross-species reciprocal-best-hit gene correspondences, local-collinearity analyses, candidate-prioritization tables, and KEGG pathway enrichment and permutation analyses. The analysis identified 20,795 apple-centered gene correspondences and prioritized 269 expression-supported candidates, 190 locally collinear candidates, 24 candidates supported by external apple leaf transcriptomes, and five candidates supported in both external leaf contexts. The dataset also contains frozen pathway mappings, supplementary numerical tables, and reproducibility documentation. Original raw sequencing reads and reference genome sequences are not redistributed; their source accessions and reference information are provided in the accompanying documentation. Associated analysis code is prepared separately for versioned release. The original biological replicate structure and the interpretation of conditional pathway permutations are discussed as methodological limitations. Release status: This archive is a pre-publication candidate pending final author approval, licensing confirmation, and manuscript–figure consistency checks.