Primers, MIDs, sequence formats and consensus reference sequence used in this study.

ColFol-for ColFol-rev are the Sanger primers. 454-ColFol-for and 454-Col307-rev are the primers for mass amplification. Adaptors A and B are used by the ‘454’ sequencer to attach individual DNA molecules to microscopic beads, for subsequent sequencing. MIDs (Multiplex Identifiers) are 7 bp sequences that allow different samples to be sequenced together on a single ‘454’ plate and then separated bioinformatically for downstream analysis. There is no MID with 454-Col307-rev because we only pyrosequenced from the forward direction. Row 5 is an example of a 454 read after demultiplexing with the Roche tools. The forward primer is underlined, and the reverse primer dashed underlined. The MID tag is removed during demultiplexing. Row 6 is an example of a sequence after processing of sequences to produce a file of unique sequences.