Improved inverse PCR scheme for metagenome walking

Abstract

Inverse PCR has been used for the recovery of genome regions flanking a known sequence, although its application to metagenome walking is limited due to inefficient amplification from low copy number fragments. Here we present an improved inverse PCR scheme that enables walking of rare fragments in environmental metagenomes. Our scheme includes the following steps: (i) inverse PCR in which one primer is connected to an affinity tag; (ii) affinity purification of PCR products for removing background metagenome; and (iii) nested PCR to recover target flanking regions (IAN-PCR). In a model experiment, flanking regions of a gene fragment in Ralstonia eutropha were recovered from mixtures of Ralstonia and Escherichia genomes by standard inverse PCR, inverse PCR coupled to nested PCR (IN-PCR), and IAN-PCR, showing that they were recovered when ratios of Ralstonia genome to the background Escherichia genome were greater than 10−1, 10−3, and 10−5, respectively. The utility of IAN-PCR was also examined by recovering flanking regions of PCR-amplified putative chitinase gene fragments from a groundwater metagenome, showing that IAN-PCR obtained flanking regions for more diverse gene fragments than IN-PCR. Since rare sequences are a critical element of natural genetic diversity, IAN-PCR enables access to undiscovered diverse genes in the environment.