Table 1 Characteristics and in silico performance of the best primer pairs. Primer pairs were grouped according to the expected amplicon size into three groups: S for small (≤600 bp), M for medium (600 – 1,000 bp), and L for large size (>1,000 bp). Fungal and non-fungal eukaryotic sequence coverage rates tested by in silico PCR. Individual primer sequence and characteristics are listed in the Additional file 1. For primer pairs see Additional file 2
Primer pair | Old name | Amplicon (nt) | Var. regions covered | Fungi (%) | Co-Amplif. (%) |
|---|---|---|---|---|---|
(0M/1M) | (0M/1M) | ||||
Group S | |||||
nu-SSU-1334-5´/nu-SSU-1648-3´ | FF390/FR-1 | 348 | V7, V8 | 80.4/92.7 | 0.2/5.0 |
nu-SSU-1430-5´/nu-SSU-1648-3´ | SR14R/FR-1 | 235 | V8 | 76.8/86.0 | 0.8/2.5 |
nu-SSU-0062-5´/nu-SSU-0531-3´ | TW9/GEO2 | 503 | V1, V2, V3 | 73.7/89.1 | 1.5/8.0 |
Group M | |||||
nu-SSU-0817-5′-24/nu-SSU-1648-3´ | nu-SSU-0817-5′/FR-1 | 870 | part of V4, V5, V6, V7, V8 | 75.8/86.2 | 0.5/4.5 |
nu-SSU-0777-5´/nu-SSU-1648-3´ | Basid 3/FR-1 | 904 | part of V4, V5, V6, V7, V8 | 68.3/80.8 | 2.9/14.7 |
Group L | |||||
nu-SSU-0068-5´-20/nu-SSU-1648-3´ | Fun18S1/FR-1 | 1615 | all except V9 | 82.3/90.3 | 2.3/6.8 |
nu-SSU-0550-5´/nu-SSU-1648-3´ | GEO3/FR-1 | 1133 | V4, V5, V7, V8 | 73.1/88.4 | 0.9/2.0 |