Chapter 11 Multi-locus Sequence Analysis

Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Xiaoying Rong, Ying Huang Multi-locus sequence analysis (MLSA) is now established as a powerful phylogenetic approach for defining the taxonomic structure and evolutionary history of diverse bacteria, and for exploring population parameters that shape speciation. In this chapter, the emphasis is on practical procedures, notably MLSA schemes designed to clarify relationships within specific genera. MLSA uses data retrieved from fragmented nucleotide sequences of housekeeping genes (normally five to seven) spread across the chromosome, thereby making it possible to construct a refined framework for unravelling population structures and prokaryotic diversity at the genome level. We summarize the molecular phylogenetic method based on MLSA, implement our MLSA scheme to species assignments of representative 16S rRNA subclades within the genus Streptomyces of the phylum Actinobacteria and outline how the MLSA method unravelled pedigrees at high resolution levels among Streptomyces and other bacteria. Our MLSA scheme based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) has been shown to clarify relationships between closely related streptomycetes with a five-gene nucleotide sequence distance of 0.007 considered to be the cutoff point for the delineation of species within this genus. Prokaryotic diversity unravelled by MLSA to a considerable extent predicts the diversity of the functiona...

Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research