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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 (600–1000 bp), and L for large size (> 1000 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

From: A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms

Primer pairOld nameAmplicon (nt)Variable regions coveredFungi (%)
(0 M/1 M)
Co-Amplif. (%)
(0 M/1 M)
Group S
 nu-SSU-1333-5′/nu-SSU-1647-3′FF390/FR-1348V7, V880.4/92.70.2/5.0
 nu-SSU-1429-5′/nu-SSU-1647-3′SR14R/FR-1235V876.8/86.00.8/2.5
 nu-SSU-0062-5′/nu-SSU-0531-3′TW9/GEO2503V1, V2, V373.7/89.11.5/8.0
Group M
 nu-SSU-0817-5′-24/nu-SSU-1647-3′nu-SSU-0817-5′/FR-1870part of V4, V5, V6, V7, V875.8/86.20.5/4.5
 nu-SSU-0777-5′/nu-SSU-1647-3′Basid 3/FR-1904part of V4, V5, V6, V7, V868.3/80.82.9/14.7
Group L
 nu-SSU-0068-5′-20/nu-SSU-1647-3′Fun18S1/FR-11615all except V982.3/90.32.3/6.8
 nu-SSU-0550-5′/nu-SSU-1647-3′GEO3/FR-11133V4, V5, V7, V873.1/88.40.9/2.0
  1. Amplicon (nt) Length of generated amplicon
  2. Fungi (%), coverage rate of fungal sequences with zero (0 M) and one (1 M) mismatch
  3. Co-Amplif. (%) Non-fungal eukaryotic co-amplification rate under a zero (0M) and one (1M) mismatch stringency