**Table S3.** Most frequently observed hits to the NR database among
unassembled reads and small scaffolds (\<10 kb), organized by Kingdom or
Superkingdom (where Kingdom is undefined). Origin: A, possible plant
associate; C, likely contaminant, U, unknown.

  ------------- ----------------------- ------------- --------------- ------------
  **Kingdom**   **Genus**               **Species**   **Sequences**   **Origin**

  Archaea       Thermoplasma            2             13              U

  Archaea       Picrophilus             1             11              U

  Archaea       Haloarcula              1             1               U

  Archaea       Methanosaeta            1             1               U

  Archaea       Methanothermobacter     1             1               U

  Bacteria      Ralstonia               7             2938            A

  Bacteria      Escherichia             1             2031            C

  Bacteria      Bordetella              3             1192            C

  Bacteria      Cupriavidus             3             975             A

  Bacteria      Xanthomonas             6             822             A

  Bacteria      Pseudomonas             15            673             A

  Bacteria      Rhodobacter             2             594             A

  Bacteria      Burkholderia            10            558             A

  Bacteria      Chromobacterium         1             359             A

  Bacteria      Mesorhizobium           4             312             A

  Bacteria      Acinetobacter           6             252             A

  Bacteria      Acetobacter             1             212             A

  Bacteria      Azoarcus                3             179             A

  Bacteria      Bradyrhizobium          2             177             A

  Bacteria      Sinorhizobium           1             163             A

  Bacteria      Haemophilus             2             149             C

  Bacteria      Pasteurella             1             135             C

  Bacteria      Brucella                1             125             C

  Bacteria      Caulobacter             1             115             A

  Bacteria      Leptospira              1             22              U

  Bacteria      Treponema               1             3               U

  Bacteria      Borrelia                1             2               U

  Fungi         Ustilago                1             91              A

  Fungi         Gibberella              2             57              A

  Fungi         Neurospora              1             40              U

  Fungi         Crinipellis             1             35              U

  Fungi         Suillus                 4             29              A

  Fungi         Schizophyllum           1             24              U

  Fungi         Magnaporthe             1             20              A

  Fungi         Armillaria              7             15              A

  Fungi         Phanerochaete           1             15              U

  Fungi         Agrocybe                1             14              U
  ------------- ----------------------- ------------- --------------- ------------