Data for the <i>Populus tremula</i> v2.2. genome project and associated genome-wide association study

<b>Background to the study:</b> We have produced a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts in 37,184 genes. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly and existing whole genome re-sequencing data to perform genome-wide association<i> </i>analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) in the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin, and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network, which we used to explore the functions of candidate genes identified from the GWAS.<br><br><b>This data set comprises: </b>the ATAC-Seq peaks from the ATAC-Sequencing of aspen leaves, '<b>Aspen leaf ATAC_Seq peaks</b><b>.zip'</b>; and the gene expression matrix of mean values per aspen genotype from the SwAsp collection, '<b>Gene_Expression_matrix_genotype_mean.tsv'</b>. We provide a zipped directory for each of '<b>ScotAsp.zip'</b>, '<b>SwAsp.zip'</b> and '<b>UmAsp.zip'</b> providing the raw leaf image scans, the cropped leaf images and raw data files from the LAMINA leaf shape analyses of these images, and the processed data files and genotypic BLUP values for each of these ScotAsp, SwAsp and UmAsp collections. We provide the GWAS associations of SNPs ranked by decreasing P-value until the 1000th gene for each of the 26 leaf physiognomy traits for each collection, i.e. '<b>ScotAsp top-ranked GWAS results'</b><b>, '</b><b>SwAsp top-ranked GWAS</b><b> results'</b> and '<b>Um</b><b>Asp top-ranked GWAS results'</b>. The single nucleotide polymorphism (SNP) data for each of the aspen collections is in <b>'</b><b>ScotAsp_biallelic_Het.HWE.recode.vcf</b><b>.gz</b><b>'</b><b>, 'SwAsp_AfterBatchRemoval_biallelic_Het.HWE.recode.vcf.gz' </b>and<b> 'UmAsp_biallelic_Het.MAF.HWE.recode_.vcf.gz'.</b>

研究背景：本研究通过长读长测序、光学图谱及高密度遗传图谱构建了染色体级别基因组组装结果，共注释39894个基因，其中37184个基因对应73765条转录本的功能注释。我们对包含227株欧洲山杨个体的于默奥山杨（Umeå Aspen, UmAsp）样本集开展了全基因组重测序。利用该组装结果与已有的全基因组重测序数据，我们针对UmAsp、瑞典山杨（Swedish Aspen, SwAsp）与苏格兰山杨（Scottish Aspen, ScotAsp）三个样本集的叶片形态表型，基于单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）开展了全基因组关联分析（Genome-Wide Association Analysis, GWAS）。通过转座酶可及性染色质测序（Assay of Transposase Accessible Chromatin sequencing, ATAC-Seq），我们鉴定得到染色质可及性基因组区域，并将SNP位点筛选限定至该区域内，由此提升了GWAS的检出效率。我们在叶片样本中筛选得到候选长链非编码RNA，并在更新后的共表达网络中对其表达量进行定量，以此探究GWAS所鉴定候选基因的功能。<br><br><b>本数据集包含：</b>山杨叶片ATAC-Seq峰文件，即文件<b>Aspen leaf ATAC_Seq peaks.zip</b>；以及来自SwAsp样本集的山杨各基因型均值基因表达矩阵，即文件<b>Gene_Expression_matrix_genotype_mean.tsv</b>。我们提供三个压缩目录：<b>ScotAsp.zip</b>、<b>SwAsp.zip</b>与<b>UmAsp.zip</b>，其中包含各样本集的原始叶片图像扫描件、裁剪后的叶片图像，以及基于这些图像通过LAMINA叶片形态分析得到的原始数据文件；同时还包含各样本集的处理后数据文件与基因型最佳线性无偏预测（Best Linear Unbiased Prediction, BLUP）值。针对每个样本集的26项叶片形态表型，我们提供了按P值降序排列的SNP关联分析结果，直至第1000个基因，对应文件分别为<b>ScotAsp top-ranked GWAS results</b>、<b>SwAsp top-ranked GWAS results</b>与<b>UmAsp top-ranked GWAS results</b>。各山杨样本集的单核苷酸多态性（SNP）数据分别存储于以下文件：<b>ScotAsp_biallelic_Het.HWE.recode.vcf.gz</b>、<b>SwAsp_AfterBatchRemoval_biallelic_Het.HWE.recode.vcf.gz</b>以及<b>UmAsp_biallelic_Het.MAF.HWE.recode_.vcf.gz</b>。