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Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

dataset
posted on 25.08.2022, 12:24 authored by Verena KutscheraVerena Kutschera, Marcin Kierczak, Tom van der ValkTom van der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne Dehasque, David W. G. Stanton, Payam Emami Khoonsari, Björn Nystedt, Love Dalén, David Díez del molinoDavid Díez del molino

This item contains a test dataset based on Sumatran rhinoceros (Dicerorhinus sumatrensis) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets.

We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (Dicerorhinus sumatrensis harrissoni; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (Ceratotherium simum simum; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode.

The test dataset contains whole-genome re-sequencing data from three historical and three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or elsewhere in the genome.

For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of years) from timetree.org is available.

Finally, the item contains configuration and metadata files that were used for three separate runs of GenErode to generate the results presented in Kutschera et al. (2022).

Bash scripts and a workflow description for the test dataset generation are available in the GenErode GitHub repository (https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation).


References:

Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022;23:228. https://doi.org/10.1186/s12859-022-04757-0

von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, et al. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications 2021;12:2393.

Funding

Knut and Alice Wallenberg Foundation (National Bioinformatics Infrastructure Sweden at SciLifeLab)

Swiss National Science Foundation (P2SKP3_165031)

Swiss National Science Foundation (P300PA_177845)

Carl Tryggers Foundation (CTS 19:257)

Historic response of a wide-ranging carnivore to climate change

European Commission

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Evolutionary dynamics of genome erosion in the woolly mammoth

Swedish Research Council

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FORMAS (2015-676)

Carl Tryggers Foundation (CTS 17:109)

SNIC 2.0: Swedish National Infrastructure for Computing

Swedish Research Council

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History

Publisher

National Bioinformatics Infrastructure Sweden (Stockholm University & Science for Life Laboratory)