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Protein-Coding Genes as Alternative Markers in Microbial Diversity Studies

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Encyclopedia of Metagenomics

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Synonyms

Automated Phylogenomic Inference Application (AMPHORA)

Introduction

The small ribosomal unit RNA (SSU rRNA or 16S rRNA) has been widely used in microbial systematic and diversity studies. The appeal of using 16S rRNA gene as a marker gene is numerous. First of all, it is distributed in every single cellular organism. Secondly, because regions of 16S rRNA sequence are highly conserved, 16S rRNA gene can be PCR amplified from a wide diversity of taxa using “universal” primers and sequenced, bypassing the need to isolate and culture the organisms in question. Consequently, millions of 16S rRNA reference sequences are available for microbial classification and identification (Cole 2009).

Although 16S rRNA has been the “gold standard” in microbial diversity studies, it has several shortcomings. First, because 16S rRNA only makes up a tiny fraction of a genome (~0.1 %), its application as a marker gene in classifying metagenomic sequences is seriously limited. Secondly, the widely...

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Authors and Affiliations

  1. Department of Biology, University of Virginia, 485 McCormick Road, 400328, Charlottesville, VA, 22903, USA

    Martin Wu

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  1. Martin Wu
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Correspondence to Martin Wu .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

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Wu, M. (2013). Protein-Coding Genes as Alternative Markers in Microbial Diversity Studies. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_734-3

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  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_734-3

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

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