Supplementary Online Material for "Coal-Miner: a statistical method for GWA studies of quantitative traits with complex evolutionary origins"

Supplementary Online Material for the manuscript entitled "Coal-Miner: a statistical method for GWA studies of quantitative traits with complex evolutionary origins"

Scheme of the metadata annotation workflow.

<p>Shaded boxes indicate procedures performed and/or saved over the PlutoF workbench (<a href="http://plutof.ut.ee/" target="_blank">http://plutof.ut.ee/</a>).</p

Quality and metadata annotations of fungal ITS sequences by mycorrhiza types.

1<p>all sequences belonging to EcM lineages regardless of isolation source;</p>2<p>all sequences belonging to Glomeromycota, except <i>Geosiphon;</i></p>3<p>all sequences derived from roots (with or without a culturing step) of the respective host plants;</p>4<p>Chimeric sequences consist of two or more fragments of fungal sequences and are therefore not assigned below the kingdom level;</p>5<p>nd, not determined;</p>6<p>Annotated–sum of original annotations and metadata provided in the course of this study;</p>7<p>formation of coils in ErM, formation of pelotons, stimulation of germination or development in OM.</p

Contribution of different isolation sources to the number of INSD sequences in the most common ectomycorrhizal fungal lineages.

<p>Contribution of different isolation sources to the number of INSD sequences in the most common ectomycorrhizal fungal lineages.</p

Screenshot of the UNITE search page (http://unite.ut.ee/).

<p>This search tool allows queries of sequences based on taxonomic information and associated metadata.</p

Ectomycorrhizal contaminants on experimental roots

These ectomycorrhizal roots were selected and sequenced by ME Smith, RA Healy and GM Bonito in May of 2011. They come from sequenced root tips from axenically grown seedlings that were inoculated with mitospores, and then transferred to a growth chamber including other inoculated plants. None of the mitospore phylotypes were recovered from root tips, but three contaminant ectomycorrhizal species were sequenced from the roots. We think they came from water splash during watering of adjacent pots that had been purposely inoculated with Tuber borchii. Identifications were from ITS sequence similarity at 97%

Tuber_ITS_alignment

Tuber ITS alignment in FASTA format, Ambiguously aligned regions were excluded in GBlocks using the least stringent setting (Castresana, 2000; Talavera & Castresana, 2007), missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM")

Hydnobolites_ITS_alignment

This is an alignment of ITS sequences (ITS1, 5.8s, ITS2) from fruit bodies, ectomycorrhizal roots and mitotic spore mats

Pezizaceae_LSU_alnmnt

Pezizaceae LSU alignment in FASTA format, missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM"

PezizalesExclPezizaceaeLSU

Pezizales exclusive of Pezizaceae LSU alignment in FASTA format, missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM"