Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens

Molecular Ecology Resources
Bastian GreshakeIngo Ebersberger

Abstract

Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide...Continue Reading

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References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 10, 2003·Bioinformatics·Mario Stanke, Stephan Waack
Jun 18, 2005·Bioinformatics·Alkes L PricePavel A Pevzner
Feb 21, 2007·Bioinformatics·Jan KrumsiekThomas Rattei
Jan 11, 2008·BMC Bioinformatics·Andreas DöringKnut Reinert
Feb 19, 2008·Mycological Research·Imke SchmittH Thorsten Lumbsch
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Oct 9, 2008·PloS One·Daniel C RichterDaniel H Huson
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Mar 10, 2010·Genomics·Jason R MillerGranger Sutton
Dec 21, 2010·Applied and Environmental Microbiology·Scott T BatesNoah Fierer
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
Sep 20, 2011·Genome Research·Dent EarlBenedict Paten
Nov 10, 2011·Nature Biotechnology·Phillip E C CompeauGlenn Tesler
Dec 8, 2011·Genome Research·Steven L SalzbergJames A Yorke
Dec 14, 2011·Genome Research·Jared T Simpson, Richard Durbin
Dec 27, 2011·Bioinformatics·Weichun HuangGabor T Marth
Feb 18, 2012·BMC Genomics·Kerensa E McElroyTorsten Thomas
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jul 24, 2012·Nucleic Acids Research·Toshiaki NamikiYasubumi Sakakibara
Aug 24, 2012·Molecular Ecology·Martin Grube, Toby Spribille
Jan 30, 2013·Nature Reviews. Genetics·Niranjan Nagarajan, Mihai Pop
Feb 13, 2013·BMC Genomics·Sergey I NikolenkoMax A Alekseyev
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
May 15, 2013·Bioinformatics·Tanja MagocSteven L Salzberg
May 31, 2013·Genome Biology·Michael G RossDavid B Jaffe
Jun 5, 2013·Bioinformatics·Rayan Chikhi, Paul Medvedev
Jul 31, 2013·Proceedings of the National Academy of Sciences of the United States of America·Annette KampaÓlafur S Andrésson
Mar 13, 2014·Molecular Ecology Resources·Pierre-Jean G MaléJérôme Chave
May 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
May 23, 2014·Nature·Kevin J ForsbergGautam Dantas
Jun 21, 2014·Bioinformatics·Bahlul HaiderChongle Pan
Nov 18, 2014·Nature Methods·Benjamin BuchfinkDaniel H Huson
Feb 26, 2015·Frontiers in Microbiology·Armin ErlacherGabriele Berg
Mar 20, 2015·Briefings in Bioinformatics·Jürgen JänesErnest Turro
Mar 18, 2016·Journal of Phycology·Debashish BhattacharyaHwan Su Yoon

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Citations

Apr 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Georgios KoutsovoulosMark Blaxter
Mar 13, 2020·Genome Biology and Evolution·Bastian Greshake TzovarasIngo Ebersberger
May 12, 2020·Microbial Genomics·Arwyn EdwardsSara M E Rassner
Apr 13, 2021·Computational and Structural Biotechnology Journal·Chaofang ZhongKang Ning

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