TABLE 2

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

Taxonomic assignmentbNo. of sequences% of sequences
Total8,439
Ascomycota2,61030.92
        Archaeorhizomycetes20.02
        Dothideomycetes1,27215.07
        Eurotiomycetes540.64
        Incertae sedis20.02
        Lecanoromycetes50.06
        Leotiomycetes1712.03
        Orbiliomycetes00
        Pezizomycetes1121.33
        Saccharomycetes110.13
        Sordariomycetes7859.30
        Unidentified1962.32
Basidiomycota1,71220.3
        Agaricomycetes1,56018.49
        Atractiellomycetes260.31
        Cystobasidiomycetes30.04
        Exobasidiomycetes00
        Microbotryomycetes230.27
        Pucciniomycetes10.01
        Tremellomycetes300.36
        Ustilaginomycetes00
        Unidentified690.82
Glomeromycota3,39040.17
        Glomeromycetes3,29439.03
        Unidentified961.14
Zygomycota
        Incertae sedis50.06
Unidentified7228.56
  • a Fungal 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).

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