Supplementary dataset to "A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses"

SUPPLEMENTARY DATASETS TO: <strong>A new genome allows the identification of genes associated with natural variation in aluminium tolerance in <em>Brachiaria </em>grasses</strong> <strong>Supplementary File 1:</strong> Cumulative root length (RL), root biomass (RB), and root tip diameter (RD) during Al³⁺ stress (A) and control (C) conditions, and the ratio (R) between stress and control values, in the interspecific progeny between CIAT 606 and BXR 44-02. <strong>Supplementary File 2: </strong>Gene annotation in GFF3 format. <strong>Supplementary File 3: </strong>Functional annotation of the genes, including GO terms and homologous proteins in NCBI nr database, Uniprot, <em>A. thaliana</em>, rice, <em>P. halli</em>, <em>S. italica</em> and <em>S. viridis</em><em>.</em> <strong>Supplementary File 4: </strong>Assignment of the proteins in the Poaceae family to eggNOG orthologous groups to identify shared clusters of proteins among these species. <strong>Supplementary File 5:</strong> Anchoring 21,145 <em>Brachiaria ruziziensis</em> scaffolds longer than 10 Kbp or with at least one annotated gene (533.9 Mbp) in <em>S. italica </em>nine chromosomes. <strong>Supplementary File 6:</strong> Chromosomal position of the 41,974 transcripts in <em>Brachiaria ruziziensis</em> based on the synteny with the <em>S. italica</em> genome. In BED5 format. <strong>Supplementary File 7: </strong>Genetic map with 4,427 markers placed at LOD 10 in 18 linkage groups, including the position of each marker in the genetic map and genome assembly. <strong>Supplementary File 8:</strong> Functional annotation of the 84 DE genes within QTLs. <strong>Supplementary File 9:</strong> Enrichment analysis of the GO terms (full ontology) over-represented among DE genes in each species with the biological processes (BP) and molecular functions (MF). <strong>Supplementary File 10:</strong> Enrichment analysis of the GO SLIM terms (reduced ontology) over-represented among DE genes in each species with the biological processes (BP) and molecular functions (MF). Margaret Worthington^1#, Juan Guillermo Perez¹, Saule Mussurova², Alexander Silva-Cordoba¹, Valheria Castiblanco¹, Juan Andres Cardoso Arango¹, Charlotte Jones³, Narcis Fernandez-Fuentes³, Leif Skot³, Sarah Dyer^2&amp;, Joe Tohme¹, Federica Di Palma², Jacobo Arango¹, Ian Armstead³, Jose J De Vega² 1. International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia. 2. Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. 3. Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK.<strong>配套补充数据集：《全新基因组助力鉴定臂形草（<em>Brachiaria</em>）属植物铝耐受性自然变异相关基因》</strong> <strong>补充文件1：</strong>记录CIAT 606与BXR 44-02种间杂种后代在铝离子（Al³+）胁迫（A组）与对照（C组）条件下的总根长（RL）、根生物量（RB）和根尖直径（RD），以及胁迫组与对照组的数值比值（R）。 <strong>补充文件2：</strong>GFF3格式的基因注释文件。 <strong>补充文件3：</strong>基因功能注释文件，包含基因本体（GO）术语，以及NCBI非冗余（nr）数据库、UniProt、拟南芥（<em>A. thaliana</em>）、水稻、<em>P. halli</em>、谷子（<em>S. italica</em>）和青狗尾草（<em>S. viridis</em>）中的同源蛋白信息。 <strong>补充文件4：</strong>将禾本科（Poaceae）家族蛋白归类至eggNOG直系同源组，以鉴定这些物种间共有的蛋白簇。 <strong>补充文件5：</strong>将21145个鲁兹臂形草（<em>Brachiaria ruziziensis</em>）序列支架锚定至谷子（<em>S. italica</em>）的9条染色体上，这些支架长度均大于10 Kbp，或至少包含1个注释基因，总组装长度达533.9 Mbp。 <strong>补充文件6：</strong>基于与谷子（<em>S. italica</em>）基因组的共线性分析，获取鲁兹臂形草（<em>Brachiaria ruziziensis</em>）41974条转录本的染色体位置信息，文件格式为BED5。 <strong>补充文件7：</strong>包含4427个标记的遗传图谱，该图谱以LOD值10进行分组，共涉及18个连锁群，文件包含每个标记在遗传图谱和基因组组装中的位置信息。 <strong>补充文件8：</strong>数量性状位点（QTL）内84个差异表达基因（DE genes）的功能注释文件。 <strong>补充文件9：</strong>对各物种差异表达基因中富集的完整版基因本体（GO）术语进行富集分析，涵盖生物过程（BP）和分子功能（MF）两个本体分支。 <strong>补充文件10：</strong>对各物种差异表达基因中富集的精简版基因本体（GO SLIM）术语进行富集分析，涵盖生物过程（BP）和分子功能（MF）两个本体分支。 <strong>作者信息：</strong>Margaret Worthington^1#、Juan Guillermo Perez¹、Saule Mussurova²、Alexander Silva-Cordoba¹、Valheria Castiblanco¹、Juan Andres Cardoso Arango¹、Charlotte Jones³、Narcis Fernandez-Fuentes³、Leif Skot³、Sarah Dyer^2*、Joe Tohme¹、Federica Di Palma²、Jacobo Arango¹、Ian Armstead³、Jose J De Vega² 1. 国际热带农业中心（CIAT），哥伦比亚卡利，航空邮政信箱6713； 2. 厄勒姆研究所（Earlham Institute），英国诺里奇诺里奇研究园，NR4 7UZ； 3. 阿伯里斯特威斯大学生物、环境与乡村科学研究所（IBERS），英国阿伯里斯特威斯。