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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