Comprehensive curation and validation of genomic datasets for chestnut [2]

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. Somatic embryo and callus dataset. In addition, third-party reanalysis of RNA-Seq samples from SRA database (see TABLE below).

板栗（Castanea mollissima）是兼具重要生态与经济价值、优良营养品质且天然抗病虫害的优质植物。近年来，高通量技术的快速发展推动了板栗基因组数据的持续积累，为该物种的遗传研究与性状改良带来了广阔前景。为提升此类数据的可访问性与实用性，我们整理并验证了一套包含8个栗属（Castanea）物种、213份RNA测序（RNA-Seq）样本及348份重测序样本的基因组数据集。该数据集已在figshare平台公开，可为从事栗属遗传学、功能基因组学与进化生物学研究的科研人员提供可靠的研究资源。此外，栗属基因组数据库（Castanea Genome Database, CGD，http://castaneadb.net）作为补充平台，提供了包括BLAST、批量查询、GO/KEGG富集分析及共线性视图（Synteny Viewer）在内的高级数据挖掘与分析工具，以优化该整理数据集的易用性。本研究利用RNA测序分析了胚、体细胞胚、愈伤组织、根及混合样本的基因表达差异；除表格中所列样本外，还纳入了181份第三方来源的样本。RNA-Seq测序读段通过FastQC（v0.11.9）完成质量控制，经Trimmomatic进行序列修剪，通过STAR（v2.7.10b）完成序列比对，并归一化至FPKM值。体细胞胚与愈伤组织数据集。此外，本研究还对SRA数据库中的第三方RNA-Seq样本进行了重新分析（详见下表）。