S1 fungus_CROP_R_script_nonrarefied

The HTML outputs of the R scripts using the non-rarefied CROP dataset

Datasets

This .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript

Bioinformatic command script

An example bioinformatic scrip

S1 fungus_uclust_R_script_nonrarefied

The HTML outputs of the R scripts using the non-rarefied UCLUST dataset

Heat map of the percentage representation of the 27 Collembola genomes within each of the 5 genomic pools, and within each of the three MID tag pools derived from each of the 5 genomic pools.

<p>For visual clarity, percentage representation of 2% or more is presented as maximum representation. See Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone-0057615-t001" target="_blank">Table 1</a> to see the actual percentages of each sequence found, and species names.</p

Regression analyses of the percentage of collembolan mtDNA COI sequences within an MID tag pool (<i>y</i> axis) against the percentage of genomic template from which they are derived within an experimental genomic pool (<i>x</i> axis).

<p>Data come from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone.0057615.s003" target="_blank">Table S1</a>. The panels from top to bottom are MID1 against pool 1, MID4 against pool 2, and MID7 against pool 3.</p

otutable_first200_tax

Top 200 most reads OTUs with their taxonomy assignment and reads numbe

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

<p>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.</p

S1 fungus_uclust_R_script_rarefied

The HTML outputs of the R scripts using the rarefied UCLUST dataset

Denoising of mtDNA COI amplicons generated from community samples of Collembola from two forest sites on the island of Tenerife with the pipeline of Yu <i>et al.</i> (2012).

<p>Steps 1–3 represent reduction of unique sequence volume by denoising, while steps 4 and 5 further reduce unique sequence volume by the creation of summary clusters of sequences. See Yu <i>et al.</i> (2012) for a detailed explanation of each of the steps. Bracketed values in step 2 represent sequences inferred to be chimeras with the <i>de novo</i> chimera detection function UCHIME in USEARCH, all of which were removed in step 4 of PyroClean.</p