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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Nature Protocols volume 9, pages 1056–1082 (2014)Cite this article

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Abstract

Next-generation sequencing technologies have revolutionized the field of paleogenomics, allowing the reconstruction of complete ancient genomes and their comparison with modern references. However, this requires the processing of vast amounts of data and involves a large number of steps that use a variety of computational tools. Here we present PALEOMIX (http://geogenetics.ku.dk/publications/paleomix), a flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. Starting with next-generation sequencing reads, PALEOMIX carries out adapter removal, mapping against reference genomes, PCR duplicate removal, characterization of and compensation for postmortem damage, SNP calling and maximum-likelihood phylogenomic inference, and it profiles the metagenomic contents of the samples. As such, PALEOMIX allows for a series of potential applications in paleogenomics, comparative genomics and metagenomics. Applying the PALEOMIX pipeline to the three ancient and seven modern Phytophthora infestans genomes as described here takes 5 d using a 16-core server.

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Figure 1
Figure 2: The P. infestans phylogeny produced by the phylogenetic pipeline on the basis of coding sequences with at least 80% of bases covered in the multiple sequence alignment.
Figure 3: Analyses of the microbial taxonomical profiles of three Phytophthora-infected historical potato samples.

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Acknowledgements

This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU); the Danish National Research Foundation (DNRF94); a Marie Curie Career Integration grant (FP7 CIG-293845); and the Marie Curie FP7 Initial Training Network (EUROTAST). The work of M.S. was made possible thanks to the support of the Lundbeck foundation (R52-A5062). A.G. and L.E. were supported by Marie Curie Intra-European Fellowships (FP7 IEF-299176 and IEF-302617, respectively). R.F. was supported by a postdoctoral grant from AXA Research Fund (32983).

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Authors and Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Michael D Martin, Ruth Fernández, Eske Willerslev & Ludovic Orlando

  2. Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, Minnesota, USA

    Robert Schaefer

  3. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    Martin Kircher

  4. College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA

    Molly McCue

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Contributions

M.S., H.J., A.G. and L.O. designed the BAM pipeline, with feedback from R.S. and M.M. M.S., A.G. and L.O. designed the phylogenetic pipeline. M.S. wrote the scripts for both pipelines, based in part on code written by M.K. L.E. and C.D.S. designed the metagenomic pipeline and scripts. M.D.M. guided selection and analysis of the example data sets. H.J., R.S., A.G., M.D.M., R.F., M.K., M.M. and L.O. tested the pipelines. L.O. coordinated the work. M.S., L.E., C.D.S., R.F. and L.O. wrote the manuscript with contributions from all the authors.

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Correspondence to Ludovic Orlando.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Phytophthora infestans samples. (PDF 61 kb)

Supplementary Table 2

Libraries for Phytophthora infestans samples. (PDF 98 kb)

Supplementary Table 3

Adapter sequences for Phytophthora infestans samples. (PDF 476 kb)

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Schubert, M., Ermini, L., Sarkissian, C. et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc 9, 1056–1082 (2014). https://doi.org/10.1038/nprot.2014.063

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