TABLE 2.

Summary of the endophytic data set from all peer-reviewed eukaryotic full-length ITS sequences (as of 1 August 2014)^a

Taxonomic assignmentb	No. of sequences	% of sequences
Total	8,439
Ascomycota	2,610	30.92
Archaeorhizomycetes	2	0.02
Dothideomycetes	1,272	15.07
Eurotiomycetes	54	0.64
Incertae sedis	2	0.02
Lecanoromycetes	5	0.06
Leotiomycetes	171	2.03
Orbiliomycetes	0	0
Pezizomycetes	112	1.33
Saccharomycetes	11	0.13
Sordariomycetes	785	9.30
Unidentified	196	2.32
Basidiomycota	1,712	20.3
Agaricomycetes	1,560	18.49
Atractiellomycetes	26	0.31
Cystobasidiomycetes	3	0.04
Exobasidiomycetes	0	0
Microbotryomycetes	23	0.27
Pucciniomycetes	1	0.01
Tremellomycetes	30	0.36
Ustilaginomycetes	0	0
Unidentified	69	0.82
Glomeromycota	3,390	40.17
Glomeromycetes	3,294	39.03
Unidentified	96	1.14
Zygomycota
Incertae sedis	5	0.06
Unidentified	722	8.56

^aFungal ITS sequences were retrieved from the NCBI nucleotide database by using the following search strings for the endophytic data set: “Endophyt*[ALL] AND nuccore_PubMed[Filter] AND internal[Title]” and “Mycorrhiza*[ALL] AND nuccore_PubMed[Filter] AND internal[Title].” Full-length ITS (ITS1, 5.8S, and ITS2 regions) sequences were extracted using ITSx (365) and assigned to operational taxonomic units (OTUs; definition set at 97% sequence similarity) with UCLUST (366), using the QIIME pipeline (367).

^bBased on comparison with the UNITE fungal ITS reference database (version 6) (368), using the QIIME pipeline (367).