Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
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This item contains a test dataset based on Sumatran rhinoceros (<em>Dicerorhinus sumatrensis</em>) 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 (<em>Dicerorhinus sumatrensis harrissoni</em>; 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 (<em>Ceratotherium simum simum</em>; 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). <br> 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.
本项包含一个基于苏门答腊犀牛（<em>Dicerorhinus sumatrensis</em>）全基因组重测序数据（whole-genome re-sequencing data）的测试数据集，该数据集与GenErode流程（GenErode pipeline）一同发布（https://github.com/NBISweden/GenErode；Kutschera et al. 2022），我们对其进行了大小缩减，以便用户在分析自身全基因组数据集前能够熟悉该流程。 我们从苏门答腊犀牛基因组组装（<em>Dicerorhinus sumatrensis harrissoni</em>；GenBank登录号GCA_014189135.1）中提取了长度为40,842,778 bp的scaffold（scaffold）‘Sc9M7eS_2_HRSCAF_41’，用作GenErode中的参考基因组（reference genome）。GenErode的部分步骤需要近缘物种的参考基因组，因此我们额外提供了来自白犀牛基因组组装（<em>Ceratotherium simum simum</em>；GenBank登录号GCF_000283155.1）的三个scaffold，总长度为41,195,616 bp，推测与苏门答腊犀牛scaffold‘Sc9M7eS_2_HRSCAF_41’同源，同时提供GTF格式的基因预测结果（gene predictions）。 该测试数据集包含来自已灭绝马来半岛种群的3个历史样本和3个现代苏门答腊犀牛样本的全基因组重测序数据，这些数据经过子采样得到映射至苏门答腊犀牛scaffold‘Sc9M7eS_2_HRSCAF_41’的双端测序读段（paired-end reads），以及少量随机选择的映射至苏门答腊犀牛线粒体基因组（mitochondrial genome）或基因组其他区域的读段。 针对GERP分析（GERP analyses），我们提供了来自30种哺乳动物外类群物种基因组组装的scaffold，这些scaffold与苏门答腊犀牛scaffold‘Sc9M7eS_2_HRSCAF_41’的基因预测结果存在reciprocal blast比对结果（reciprocal blast hits）。此外，还提供了白犀牛与这30种外类群物种的系统发育树（phylogeny），包括来自timetree.org的分化时间估算（单位：十亿年）。 最后，本项包含用于GenErode三次独立运行以生成Kutschera et al.（2022）中呈现结果的配置文件（configuration files）和元数据文件（metadata files）。 Bash脚本（Bash scripts）和流程说明（workflow description）可在GenErode的GitHub仓库中获取（https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation）。 <br> 参考文献： 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.
