PONE_mesquite

This data file contains 3 alignments of fungal ITS rDNA sequences and 9 alignments of fungal LSU rDNA sequences amplified and cloned from total genomic DNA isolated from Ah horizon forest soil of the Hainich-Dün Biodiversity Exploratory

Bacteria and fungal community dynamics in decomposing litter

The data files include (i) biom matrix for bacteria 16S (ii) biom matrix for fungi ITS (iii) representative sequence for bacteria (iv) representative sequence for fungi (v) bioinformatic script for bacteria and (vi) bioinformatic script for fung

Characteristics of primers and primer pairs.

<p>*f = forward, r = reverse;</p><p>**melting temperatures (Tm) of oligonucleotide sequences were calculated using Oligo Analysis Tool (<a href="http://www.operon.com/tools/oligo-analysis-tool.aspx" target="_blank">http://www.operon.com/tools/oligo-analysis-tool.aspx</a>),</p><p>***percentage values estimated from the total cloning/sequencing approach adopted in other biodiversity studies on sampled forest soils (ITS: 567, Mix5: 986, Mix7: 1117 sequences).</p

MEGA 4.0.2-derived phylogenetic relationships between sequences within the Mix7 T1-0.05 dataset demonstrated at the FastGroupII-defined OTU level (unrooted ME trees, 100 bootstrap replicates, K2P model). Bootstrap values >50 are highlighted.

<p>OTUs are named and represented as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032139#pone-0032139-g006" target="_blank">Figure 6</a>; i = near <i>Melanogaster variegatus</i> DQ534668, j, k = near <i>Tremellodendron sp. PBM2324</i> AY745701.</p

DAMBE substitution saturation plots for A) ITS, B) Mix5, C) Mix7 sequence datasets (unaltered T1-0.05 alignments).

<p>The number of transitions (s) and transversions (t) is plotted against the K2P distance; lines indicate the mean values (thick lines) and standard deviations (fine lines) of s and v.</p

Recovery of higher-level phylogenetic groups with OTUs identified using BLAST searches for the T1-0.05 alignments.

<p>Neighbor-joining was performed with the BioNJ algorithm as implemented in SeaView v.4.2.3 using the K2P model and 100 bootstrap pseudoreplicates; gaps were ignored. Dendroscope v.2.6.1 was used to prepare circular representations of the phylogenetic trees. Bootstrap values for supported groups are given at the appropriate node, along with average bootstrap values for supported higher taxonomic groups (internal average bootstrap scores are shown under the appropriate taxon label) and across the entire alignment (in the center of the tree). The width of each coloured block close to the circumference of the trees is exactly equal to the number of individual sequences representing the appropriate phylogenetic group; * OTU contains an ITS sequence of uncertain taxonomy (MycoBank MB19330: Agaricales, NCBI Taxonomy ID 178442: Boletales, Index Fungorum LSID 19330: Russulales) that makes the monophyly of the Boletales clade questionable (and therefore not bootstrap supported in the ITS tree).</p

MEGA 4.0.2-derived phylogenetic relationships between sequences within the ITS T1-0.05 dataset at the FastGroupII-defined OTU level (unrooted ME trees, 100 bootstrap replicates, K2P model).

<p>Bootstrap values >50 are highlighted. OTU names include the genus, number of sequences, and most relevant BLAST hit(s) with NCBI annotation(s): a = near <i>Naucoria escharoides</i> AY900084, b = near <i>Rhizoctonia sp.</i> Eab-S1 AJ242881, c = near <i>Ganoderma lipsiense</i> EF060006, d = near <i>Russula cyanoxantha</i> AY606960, e = near <i>R. sp.</i> MHM078 EU569265, f = near <i>R. farinipes</i> DQ421983, g = near <i>Cryptococcus podzolicus</i> AJ581036, h = near <i>Hygrocybe aff. conica</i> PBM 918 AY854074. Singleton OTUs are denoted by thick pale branch lines; multisequence OTUs are represented as blocks (their widths correspond to their maximum internal distance).</p

FastGroupII derived rarefaction analysis of 4 sequence datasets using different alignment treatments and cutoff levels: A) ITS, B) Mix5, C) Mix7, and D) a combined Mix5+7 LSU dataset.

<p>FastGroupII derived rarefaction analysis of 4 sequence datasets using different alignment treatments and cutoff levels: A) ITS, B) Mix5, C) Mix7, and D) a combined Mix5+7 LSU dataset.</p

High-level (family and order) diversity of the FastGroupII derived OTUs for the T1-0.05 alignments (5% OTU cutoff, gaps and ambiguities not treated) for A) ITS, B) Mix5, and C) Mix7.

<p>High-level (family and order) diversity of the FastGroupII derived OTUs for the T1-0.05 alignments (5% OTU cutoff, gaps and ambiguities not treated) for A) ITS, B) Mix5, and C) Mix7.</p

Location of the new Mix5 and Mix7 primer pairs in relation to the ITS4B primer and the 28S (LSU) RDN25-1 gene from the <i>Saccharomyces cerevisiae</i> genome, with the more diverse D regions annotated.

<p>The ClustalX conservation score for the Mix5+7 alignment is shown in grey.</p