Data from: Whole-genome analysis of giraffe supports four distinct species

The data deposited here was generated by and reported in Coimbra <em>et al</em>. (2021). <em>Annotation of the Kordofan giraffe genome assembly:</em> <strong>SGN_Gcam_PLA01_asm_pseudohap.final.gtf.gz</strong>: annotation of protein-coding genes generated with BRAKER using protein sequences from Bos taurus (GCA_002263795.2) as extrinsic evidence. <strong>SGN_Gcam_PLA01_asm_pseudohap.final.cds.all.fa.gz</strong>: coding sequences of the annotated genes (including alternative transcripts). <strong>SGN_Gcam_PLA01_asm_pseudohap.final.pep.all.fa.gz</strong>: peptide sequences of the annotated genes (including alternative transcripts). <strong>SGN_Gcam_PLA01_asm_pseudohap.final.repeatmasker.out.gz</strong>: annotation of repetitive elements generated with RepeatMasker and RepeatModeler. <em>Nuclear phylogenomic inference:</em> <strong>genomefragments.tar.gz</strong>: main dataset of 1,068 genome fragment (GF) alignments, each 450 kbp in length, with 43 giraffe (<em>Giraffa</em> spp.) and an okapi (<em>Okapia johnstoni</em>). The genome consensus sequences and subsequent processed genome fragment alignments were generated from BAM files following the method described in the article. <strong>estimated_gene_trees.tree</strong>: list containing the 1,068 maximum likelihood GF trees inferred with IQ-TREE. <strong>estimated_species_trees.tree</strong>: multispecies coalescent tree inferred by ASTRAL from the 1,068 maximum likelihood GF trees listed in <em>'estimated_gene_trees.tree</em>'. <strong>annotation.txt</strong>: annotation file used in the analysis of quartet frequencies with DiscoVista. <em>Phylogeny of mitochondrial genomes:</em> <strong>mtdna_alignments.tar</strong>: dataset containing alignments of the 13 mitochondrial protein coding genes, with 50 giraffe and an okapi, a nexus file specifying partitions, and the resulting maximum likelihood tree iferred in IQ-TREE. <em>Demographic reconstruction:</em> <strong>psmc_files.tar</strong>: output files of the PSMC analysis of 21 giraffe. <strong>psmc_boot_files.tar.gz</strong>: output files of the PSMC analysis with 100 bootstrap replicates. <em>Heterozygosity:</em> <strong>foldedSFS.tar</strong>: dataset containing the per-sample bootstrapped folded site frequency spectrum (SFS) of 50 giraffe individuals estimated with ANGSD and its subprogram realSFS. <em>ROH and Inbreeding:</em> <strong>giraffeROH.tar</strong>: CSV files extracted from RZooROH results: <em>roh_outputs_giraffe.csv:</em> realized inbreeding coefficient (F_ROH) per homozygosity-by-descent (HBD) class per individual. <em>giaffe_roh_sgmt.csv</em>: number and accumulated length of ROH per individual.本数据集存档内容由Coimbra等人（2021年）生成并报道。 <em>科尔多凡长颈鹿（Kordofan giraffe）基因组组装注释：</em> <strong>SGN_Gcam_PLA01_asm_pseudohap.final.gtf.gz</strong>：以牛（Bos taurus，登录号GCA_002263795.2）的蛋白质序列作为外源证据，通过BRAKER软件注释得到的蛋白质编码基因注释文件。 <strong>SGN_Gcam_PLA01_asm_pseudohap.final.cds.all.fa.gz</strong>：已注释基因的编码序列（包含可变剪接转录本）。 <strong>SGN_Gcam_PLA01_asm_pseudohap.final.pep.all.fa.gz</strong>：已注释基因的肽段序列（包含可变剪接转录本）。 <strong>SGN_Gcam_PLA01_asm_pseudohap.final.repeatmasker.out.gz</strong>：通过RepeatMasker与RepeatModeler注释得到的重复序列元件注释文件。 <em>核基因组系统发育组学推断：</em> <strong>genomefragments.tar.gz</strong>：核心数据集包含1068条基因组片段（GF）比对序列，单条长度为450千碱基对，涵盖43头长颈鹿属（Giraffa spp.）个体与1头霍加狓（Okapia johnstoni）。基因组共识序列及后续处理得到的基因组片段比对文件，均由BAM文件按照本文所述方法生成。 <strong>estimated_gene_trees.tree</strong>：包含1068条由IQ-TREE软件推断得到的最大似然法基因组片段系统发育树的列表文件。 <strong>estimated_species_trees.tree</strong>：由ASTRAL软件基于<em>estimated_gene_trees.tree</em>中的1068条最大似然基因组片段系统发育树推断得到的多物种溯祖物种树文件。 <strong>annotation.txt</strong>：用于DiscoVista软件进行四分体频率分析的注释文件。 <em>线粒体基因组系统发育分析：</em> <strong>mtdna_alignments.tar</strong>：数据集包含13个线粒体蛋白质编码基因的比对序列，涵盖50头长颈鹿与1头霍加狓，同时包含指定序列分区的Nexus格式配置文件，以及由IQ-TREE软件推断得到的最终最大似然系统发育树。 <em>种群历史重建：</em> <strong>psmc_files.tar</strong>：21头长颈鹿的成对顺序马尔可夫溯祖（PSMC，Pairwise Sequentially Markovian Coalescent）分析输出文件集。 <strong>psmc_boot_files.tar.gz</strong>：包含100次自举重复的PSMC分析输出文件集。 <em>杂合性分析：</em> <strong>foldedSFS.tar</strong>：数据集包含50头长颈鹿个体的每样本自举折叠位点频率谱（SFS，Site Frequency Spectrum），该结果由ANGSD软件及其子程序realSFS估算得到。 <em>纯合子片段（ROH，Runs of Homozygosity）与近交分析：</em> <strong>giraffeROH.tar</strong>：从RZooROH软件分析结果提取得到的CSV格式文件： <em>roh_outputs_giraffe.csv</em>：按每个个体的同源纯合（HBD，Homozygosity-by-descent）类别划分的实际近交系数（F_ROH）。 <em>giraffe_roh_sgmt.csv</em>：每个个体的ROH数量与累计长度。