Published June 2, 2021 | Version 1.0.0
Dataset Open

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

Authors/Creators

  • 1. Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
  • 2. Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
  • 3. Smithsonian-Mason School of Conservation, Front Royal, VA, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
  • 4. Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
  • 5. Giraffe Conservation Foundation, Eros, Windhoek, Namibia
  • 6. Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany

Contributors

  • 1. Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany

Description

The data deposited here was generated by and reported in Coimbra et al. (2021).

Annotation of the Kordofan giraffe genome assembly:

  • SGN_Gcam_PLA01_asm_pseudohap.final.gtf.gz: annotation of protein-coding genes generated with BRAKER using protein sequences from Bos taurus (GCA_002263795.2) as extrinsic evidence.
  • SGN_Gcam_PLA01_asm_pseudohap.final.cds.all.fa.gz: coding sequences of the annotated genes (including alternative transcripts).
  • SGN_Gcam_PLA01_asm_pseudohap.final.pep.all.fa.gz: peptide sequences of the annotated genes (including alternative transcripts).
  • SGN_Gcam_PLA01_asm_pseudohap.final.repeatmasker.out.gz: annotation of repetitive elements generated with RepeatMasker and RepeatModeler.

Nuclear phylogenomic inference:

  • genomefragments.tar.gz: main dataset of 1,068 genome fragment (GF) alignments, each 450 kbp in length, with 43 giraffe (Giraffa spp.) and an okapi (Okapia johnstoni). The genome consensus sequences and subsequent processed genome fragment alignments were generated from BAM files following the method described in the article.
  • estimated_gene_trees.tree: list containing the 1,068 maximum likelihood GF trees inferred with IQ-TREE.
  • estimated_species_trees.tree: multispecies coalescent tree inferred by ASTRAL from the 1,068 maximum likelihood GF trees listed in 'estimated_gene_trees.tree'.
  • annotation.txt: annotation file used in the analysis of quartet frequencies with DiscoVista.

Phylogeny of mitochondrial genomes:

  • mtdna_alignments.tar: 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.

Demographic reconstruction:

  • psmc_files.tar: output files of the PSMC analysis of 21 giraffe.
  • psmc_boot_files.tar.gz: output files of the PSMC analysis with 100 bootstrap replicates.

Heterozygosity:

  • foldedSFS.tar: dataset containing the per-sample bootstrapped folded site frequency spectrum (SFS) of 50 giraffe individuals estimated with ANGSD and its subprogram realSFS.

ROH and Inbreeding:

  • giraffeROH.tar: CSV files extracted from RZooROH results:
    • roh_outputs_giraffe.csv: realized inbreeding coefficient (FROH) per homozygosity-by-descent (HBD) class per individual.
    • giaffe_roh_sgmt.csv: number and accumulated length of ROH per individual.

Notes

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.

Files

annotation.txt

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Additional details

Related works

Is supplement to
Journal article: 10.1016/j.cub.2021.04.033 (DOI)
Software: https://github.com/rtfcoimbra/Coimbra-et-al-2021_CurrBiol (URL)
Software: 10.5281/zenodo.8367893 (DOI)