Replication Data for: 'Gene gain, duplication and loss across the Metazoa Tree of Life'

Supplementary materials for the manuscript entitled 'Gene gain, duplication and loss across the Metazoa Tree of Life' by Rosa Fernández and Toni Gabaldón, published in Nature Ecology and Evolution. Documents included in this repository: Suppl. Mat. S1: Taxa included in this study. Accession numbers are indicated. Suppl. Mat. S2: Gene gain/loss values under the 'Porifera first' hypothesis. Suppl. Mat. S3: Raw values of gene gain/loss/duplication ratios for each dataset. Suppl. Mat. S4: Orthology tables for each dataset. Suppl. Mat. S5: Orthogroups inferred with OrthoFinder for each dataset. Number of duplications per taxon is indicated. Suppl. Mat. S6: GO enrichment analyses (fatiGO output files). If no enrichment was detected, no files were uploaded. Suppl. Mat. S7: eggNOG-mapper annotations of each genome and transcriptome, as well as the top 10 most duplicated orthogroups. Suppl. Mat. S8: Gene gain, duplication and loss values for each quartile of four selected phylomes to further test the effect of evolutionary rate and sequence length. Suppl. Mat. S9: Orthogroups in the metazoan gene repertoire. KEGG pathway annotation and total number of duplicates for each orthogroup are indicated. SpeciesTree_dataset2_rooted.nwk: Rooted species tree for dataset 2 (see Methods). SpeciesTree_dataset3_rooted.nwk: Rooted species tree for dataset 3 (see Methods).本材料为Rosa Fernández与Toni Gabaldón撰写、发表于《Nature Ecology and Evolution》的手稿《跨动物界生命之树的基因获得、复制与丢失》（Gene gain, duplication and loss across the Metazoa Tree of Life）的补充资料。本仓库包含以下内容： 补充材料S1：本研究纳入的类群，已标注对应的登录号（Accession numbers）。 补充材料S2：基于“海绵动物先起源”假说的基因获得/丢失数值。 补充材料S3：各数据集的基因获得、丢失与复制比率原始数值。 补充材料S4：各数据集的直系同源表。 补充材料S5：使用OrthoFinder推断得到的各数据集直系同源组，已标注每个类群的复制事件数量。 补充材料S6：基因本体（Gene Ontology，GO）富集分析结果（fatiGO工具输出文件），若无富集结果则未上传对应文件。 补充材料S7：各基因组与转录组的eggNOG-mapper注释结果，以及复制次数排名前10的直系同源组。 补充材料S8：针对4个选定系统发育组的各四分位数区间的基因获得、复制与丢失数值，用于进一步验证进化速率与序列长度的影响效应。 补充材料S9：动物界基因库中的直系同源组，已标注每个直系同源组的KEGG通路注释信息与总复制次数。 另有两个物种树文件： SpeciesTree_dataset2_rooted.nwk：数据集2的有根物种树（详见方法部分）。 SpeciesTree_dataset3_rooted.nwk：数据集3的有根物种树（详见方法部分）。