DOI: 10.5281/zenodo.4781356
title: Data from: Whole-genome analysis of giraffe supports four distinct species

description: 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<sub>ROH</sub>) per homozygosity-by-descent (HBD) class per individual. <em>giaffe_roh_sgmt.csv</em>: number and accumulated length of ROH per individual.
description: Please cite: Coimbra RTF, Winter S, Kumar V., Koepfli K-P, Gooley RM, Dobrynin P, Fennessy J, Janke A (2021) Whole-genome analysis of giraffe supports four distinct species. Current Biology, 31(13):P2929-2938.E5. https://doi.org/10.1016/j.cub.2021.04.033. Funding: The present study is a product of the Centre for Translational Biodiversity Genomics (LOEWE-TBG) as part of the ''LOEWE—Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz'' program of Hesse's Ministry of Higher Education, Research, and the Arts as well as the Leibniz Association.