Comprehensive curation and validation of genomic datasets for chestnut

The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and validated a collection of genomic datasets for eight Castanea species, 213 RNA-Seq samples, and 348 resequencing samples. These datasets are publicly available on figshare, providing a robust resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Additionally, the Castanea Genome Database (CGD, http://castaneadb.net) serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets. This study analyzes gene expression differences in embryos, somatic embryos, callus, roots, and mixed samples using RNA sequencing, in addition to the samples provided in the table, including 181 samples obtained from third-party sources. RNA-Seq reads were processed with FastQC (v0.11.9), trimmed with Trimmomatic, aligned using STAR (v2.7.10b), and normalized to FPKM values. Mix dataset. In addition, third-party reanalysis of RNA-Seq samples from SRA database (see TABLE below).