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

Mikkel Schubert; Luca Ermini; Clio Der Sarkissian; Hákon Jónsson; Aurélien Ginolhac; Robert Schaefer; Michael D. Martin; Ruth Fernández; Martin Kircher; Molly E McCue; Eske Willerslev; Ludovic Orlando

doi:10.1038/nprot.2014.063

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

Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D. Martin, Ruth Fernández, Martin Kircher, Molly E McCue, Eske Willerslev, Ludovic Orlando

Veterinary Population Medicine

Research output: Contribution to journal › Article › peer-review

331 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1056-1082
Number of pages	27
Journal	Nature Protocols
Volume	9
Issue number	5
DOIs	https://doi.org/10.1038/nprot.2014.063
State	Published - May 2014

Bibliographical note

Funding Information:
acknoWleDGMents 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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Schubert, M., Ermini, L., Sarkissian, C. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M. E., Willerslev, E., & Orlando, L. (2014). Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols, 9(5), 1056-1082. https://doi.org/10.1038/nprot.2014.063

Schubert, M, Ermini, L, Sarkissian, CD, Jónsson, H, Ginolhac, A, Schaefer, R, Martin, MD, Fernández, R, Kircher, M, McCue, ME, Willerslev, E & Orlando, L 2014, 'Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX', Nature Protocols, vol. 9, no. 5, pp. 1056-1082. https://doi.org/10.1038/nprot.2014.063

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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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note = "Funding Information: acknoWleDGMents 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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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

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