Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

  1. Leese, Florian
  2. Brand, Philipp
  3. Rozenberg, Andrey
  4. Agrawal, Shobhit
  5. Dambach, Johannes
  6. Dietz, Lars
  7. Doemel, Jana S.
  8. Goodall-Copstake, William P.
  9. Held, Christoph
  10. Jackson, Jennifer A.
  11. Lampert, Kathrin P.
  12. Linse, Katrin
  13. Macher, Jan N.
  14. Nolzen, Jennifer
  15. Raupach, Michael J.
  16. Rivera, Nicole T.
  17. Schubart, Christoph D.
  18. Striewski, Sebastian
  19. Tollrian, Ralph
  20. Sands, Chester J.
  21. Mayer, Christoph ORCID logo

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WeightNameValue
1000 Titel
  • Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology
1000 Autor/in
  1. Leese, Florian |
  2. Brand, Philipp |
  3. Rozenberg, Andrey |
  4. Agrawal, Shobhit |
  5. Dambach, Johannes |
  6. Dietz, Lars |
  7. Doemel, Jana S. |
  8. Goodall-Copstake, William P. |
  9. Held, Christoph |
  10. Jackson, Jennifer A. |
  11. Lampert, Kathrin P. |
  12. Linse, Katrin |
  13. Macher, Jan N. |
  14. Nolzen, Jennifer |
  15. Raupach, Michael J. |
  16. Rivera, Nicole T. |
  17. Schubart, Christoph D. |
  18. Striewski, Sebastian |
  19. Tollrian, Ralph |
  20. Sands, Chester J. |
  21. Mayer, Christoph |
1000 Erscheinungsjahr 2012
1000 LeibnizOpen
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2012-11-21
1000 Erschienen in
1000 Quellenangabe
  • 7(11):e49202
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2012
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1371/journal.pone.0049202 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504011/ |
1000 Ergänzendes Material
  • http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049202#s6 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.
1000 Sacherschließung
lokal Invertebrate genomics
lokal Mitochondria
lokal Genomic libraries
lokal Sequence databases
lokal Malacology
lokal Arthropoda
lokal Animal genomics
lokal Genomic databases
1000 Fachgruppe
  1. Biologie |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/TGVlc2UsIEZsb3JpYW4=|https://frl.publisso.de/adhoc/creator/QnJhbmQsIFBoaWxpcHA=|https://frl.publisso.de/adhoc/creator/Um96ZW5iZXJnLCBBbmRyZXk=|https://frl.publisso.de/adhoc/creator/QWdyYXdhbCwgU2hvYmhpdA==|https://frl.publisso.de/adhoc/creator/RGFtYmFjaCwgSm9oYW5uZXM=|https://frl.publisso.de/adhoc/creator/RGlldHosIExhcnM=|https://frl.publisso.de/adhoc/creator/RG9lbWVsLCBKYW5hIFMu|https://frl.publisso.de/adhoc/creator/R29vZGFsbC1Db3BzdGFrZSwgV2lsbGlhbSBQLg==|https://frl.publisso.de/adhoc/creator/SGVsZCwgQ2hyaXN0b3Bo|https://frl.publisso.de/adhoc/creator/SmFja3NvbiwgSmVubmlmZXIgQS4=|https://frl.publisso.de/adhoc/creator/TGFtcGVydCwgS2F0aHJpbiBQLg==|https://frl.publisso.de/adhoc/creator/TGluc2UsIEthdHJpbg==|https://frl.publisso.de/adhoc/creator/TWFjaGVyLCBKYW4gTi4=|https://frl.publisso.de/adhoc/creator/Tm9semVuLCBKZW5uaWZlcg==|https://frl.publisso.de/adhoc/creator/UmF1cGFjaCwgTWljaGFlbCBKLg==|https://frl.publisso.de/adhoc/creator/Uml2ZXJhLCBOaWNvbGUgVC4=|https://frl.publisso.de/adhoc/creator/U2NodWJhcnQsIENocmlzdG9waCBELg==|https://frl.publisso.de/adhoc/creator/U3RyaWV3c2tpLCBTZWJhc3RpYW4=|https://frl.publisso.de/adhoc/creator/VG9sbHJpYW4sIFJhbHBo|https://frl.publisso.de/adhoc/creator/U2FuZHMsIENoZXN0ZXIgSi4=|http://orcid.org/0000-0001-5104-6621
1000 Label
1000 Förderer
  1. German Research Foundation (DFG)
  2. European Science Foundation
  3. Antarctic Science Bursary
  4. Crustacean Society
  5. Natural Environment Research Council
  6. rectorate of the Ruhr University Bochum
1000 Fördernummer
  1. LE 2323/2;MA 3684/3; SPP 1158; 1460/3, 1460/8; RA 1688/2
  2. -
  3. -
  4. -
  5. NE/DO1249X/1
  6. -
1000 Förderprogramm
  1. -
  2. “Frontiers of Speciation Research“ exchange grant
  3. -
  4. student scholarship
  5. NERC Consortium grant; British Antarctic Survey Polar Science for Planet Earth Programme
  6. scheme to support specific activities of doctoral students
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