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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 pair Old name Amplicon (nt) Variable regions covered Fungi (%)
(0 M/1 M)
Co-Amplif. (%)
(0 M/1 M)
Group S
 nu-SSU-1333-5′/nu-SSU-1647-3′ FF390/FR-1 348 V7, V8 80.4/92.7 0.2/5.0
 nu-SSU-1429-5′/nu-SSU-1647-3′ 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-1647-3′ 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-1647-3′ 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-1647-3′ Fun18S1/FR-1 1615 all except V9 82.3/90.3 2.3/6.8
 nu-SSU-0550-5′/nu-SSU-1647-3′ GEO3/FR-1 1133 V4, V5, V7, V8 73.1/88.4 0.9/2.0
  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