Illumina_Guts_Dryad_submitted_files

Illumina_Guts_Dryad_submitted_file

Eaton_PineBarrens

Eaton_PineBarren

<i>In silico</i> comparisons of DNA markers using known database sequences.

<p>(A) Nearest neighbour distances provide relative sequence divergence among species (n = 115). Letters denote significant differences (α = 0.05) and the dotted line shows 2% sequence divergence. (B) Associated accuracy of taxonomic assignments of mock sequence reads using BLAST was assessed at the genus (“G”, n = 919, 447, 432, 364) and species levels (“S”, n = 893, 420, 410, 320 for ITS2, <i>mat</i>K, <i>rbc</i>L, and <i>trn</i>L, respectively).</p

<i>In situ</i> taxonomic resolution of sequences.

<p>Log number of sequences per sample (n = 35) assigned unambiguously at the family (A), genus (B), or species (C) level versus the log number of sequences assigned at the order level are shown for four DNA markers. Lines indicate the upper limit if all sequences are resolved. Median percent of sequences per sample unassigned at each level are indicated. Roman numerals denote significant marker differences (α = 0.05) in taxonomic resolution.</p

Total numbers of vascular plant taxa that were observed across 35 soil cores with eDNA and overlap with the list of previously recorded taxa, given the database coverage.

<p>Total numbers of vascular plant taxa that were observed across 35 soil cores with eDNA and overlap with the list of previously recorded taxa, given the database coverage.</p

fastq data of the natural communities part2

D indicates the primer pair ArF2/LoboR1. 1, 2, 3 and 4 (after primers) indicate the four different natural communities. 1, 2, 3, 4 and 5 (after hyphen) indicate the five samples of each natural community

Complementarity of plant diversity reported <i>in situ</i> by the four DNA markers.

<p>Number of observations of vascular plant genera from 35 soil cores are grouped by order and arranged by established phylogenetic relationships [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157505#pone.0157505.ref034" target="_blank">34</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157505#pone.0157505.ref035" target="_blank">35</a>]. Larger plant clades are labeled and orders that were not previously recorded in surveys are indicated with asterisks.</p

<i>In situ</i> sequence recovery by DNA marker.

<p>Median number of sequences per soil sample (n = 35) recovered for each DNA marker at sequential stages of filtering in the OTU approach (A) and taxonomy approach (B). Error bars represent median absolute deviations and letters denote significant differences (α = 0.05) at each filtering stage.</p

Sequence database (GenBank) coverage of the four DNA markers summarized for both total entries and the targeted plant list.

<p>Sequence database (GenBank) coverage of the four DNA markers summarized for both total entries and the targeted plant list.</p

fastq data of the assembled communities

Mix 1, 2 and 3 indicate the three different assembled communities. Primer pairs A, B, C and D are LoboF1/LoboR1, LoboF1/250R, ArF2/ArR5 and ArF2/LoboR1, respectively