Additional Data: De Novo Annotation Reveals Transcriptomic Complexity Across the Hexaploid Wheat Pan-Genome

Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Analysis of these de novo annotations facilitated the identification of cultivar-specific genes and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. In a case study utilising both the newly constructed gene-based wheat pan-genome and pan-transcriptome, we demonstrate variation in the prolamin superfamily and immune-reactive proteins across cultivars.The datasets provided here are detailed in _README_contents.xlsx小麦是全球种植范围最广的作物，年种植总面积超过2.15亿公顷。10+小麦基因组计划（10+ Wheat Genomes Project）近期完成了9个小麦栽培品种的染色体级基因组测序与组装，揭示了小麦泛基因组（pan-genome）内的遗传多样性与选择演化特征。本研究针对上述9个小麦栽培品种，构建了包含从头注释（de novo annotation）与多组织差异表达分析的小麦泛转录组（pan-transcriptome）数据集。对上述从头注释结果的分析，助力鉴定出品种特异性基因，并明确了小麦的核心基因组（core genome）与可有可无基因组（dispensable genome）。跨品种与组织的表达谱分析显示，大量核心集合的部分同源基因（homeologous genes）在表达模式上具有保守性，但不同品种间的亚基因组（subgenome）部分同源基因表达偏向性，以及品种特异性表达谱均存在广泛差异。本研究依托全新构建的基于基因的小麦泛基因组与泛转录组开展案例分析，证实了醇溶蛋白超家族（prolamin superfamily）与免疫活性蛋白在不同栽培品种间存在变异。本数据集的详细信息详见README_contents.xlsx。