Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR

Sizhong Yang; Susanne Liebner; Mashal Alawi; Oliver Ebenhöh; Dirk Wagner

doi:10.1016/j.mimet.2014.05.006

Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR

J Microbiol Methods. 2014 Aug:103:3-5. doi: 10.1016/j.mimet.2014.05.006. Epub 2014 May 21.

Authors

Sizhong Yang¹, Susanne Liebner², Mashal Alawi², Oliver Ebenhöh², Dirk Wagner²

Affiliations

¹ GFZ German Research Centre for Geosciences, Section 4.5: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany. Electronic address: sizhong.yang@gfz-potsdam.de.
² GFZ German Research Centre for Geosciences, Section 4.5: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.

PMID: 24858450
DOI: 10.1016/j.mimet.2014.05.006

Abstract

The functional mcrA gene of methanogens can generate phylogeny as congruent as the 16S rRNA gene phylogeny. For the mcrA sequences amplified by mlas/mcrA-rev primers, we created a database for taxonomical classification and propose cut-off values for OTU clustering and further analysis of α- and β-diversity with the MOTHUR software.

Keywords: Cut-off; MOTHUR; Methanogens; Taxonomic database; mcrA gene.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Databases, Nucleic Acid*
Genes, Archaeal*
Genomics
High-Throughput Nucleotide Sequencing*
Methanomicrobiaceae / genetics*
RNA, Ribosomal, 16S / genetics
Reference Values
Software*

Substances

RNA, Ribosomal, 16S