Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

Table 2 Success of species detection using 454 pyrosequencing

Direction/run/gene	Species detected	Species missed	% Identification success rate
Run 1
COI forward	100	7	93.46
COI reverse	98	9	91.59
COI both directions	103	4	96.26
Run2
COI forward	98	9	91.59
COI reverse	101	6	94.39
COI both directions	102	5	95.33
Both runs
COI forward	101	6	94.39
COI reverse	102	5	95.33
COI both directions	103	4	96.26
Run 1
CytB forward	78	29	72.90
CytB reverse	79	28	73.83
CB both directions	83	24	77.57
run2
CytB forward	77	30	71.96
CytB reverse	80	27	74.77
CytB both directions	86	21	80.37
Both runs
CytB forward	85	22	79.44
CytB reverse	83	24	77.57
CytB both directions	89	18	83.18
Both genes for run1	105	2	98. 13
Both genes for run2	106	1	99. 07
All runs/direction/genes combined	106	1	99. 07

Species detected and missed from the ten field sites using 454 pyrosequencing examining each gene in each direction (forward or reverse) and both directions (combining forward and reverse sequences) and combining these across biological replicates (runs). The result for both genes combined in each run (biological replicate 1 and biological replicate 2) and the results for the entire experiment are bolded. Values given are based on 107 opportunities to detect a species across all ten field samples (i.e. the sum of the number of species for each of the 10 field sites).

ISSN: 1742-9994