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

The Original Article was published on 20 November 2018

Correction to: BMC Microbiol

https://doi.org/10.1186/s12866-018-1331-4

Following publication of the original article [1], we have been notified that three of the primer names identified as most promising candidates for fungal community surveys were incorrectly renamed following the primer nomenclature system proposed by Gargas & DePriest [2]. Their positioning on the reference sequence had to be shifted 1bp towards the 3’-end (see Table 1 for the correct naming). The same error occurred in some primer names listed in the additional files (see attached Supplementary information).

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

As consequence, the number of identical nucleotides shared by the most promising primers and the newly designed blocking oligo sequences changed (see Table 2).

In this correction, the revised supplementary materials are included.

Table 2 Characteristics of the best blocking oligonucleotides complementing the primer pair nu-SSU-1334-5’/nu-SSU-1648-3’ (FF390/FR-1). Fungal and non-fungal eukaryotic sequence coverage rate tested by in silico analysis

References

  1. Banos, et al. A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol. 2018;18:190. https://doi.org/10.1186/s12866-018-1331-4.

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  2. Gargas A, DePriest PT. A nomenclature for fungal PCR primers with examples from intron-containing SSU rDNA. Mycologia. 1996;88(5):745–8. https://doi.org/10.2307/3760969.

    Article  CAS  Google Scholar 

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Correspondence to Marlis Reich.

Supplementary information

Additional file 1.

List of the 164 fungi-specific primers detected by a literature research. For each primer, performance, characteristics and source literature are provided.

Additional file 2.

List of the 436 fungi-specific primer pairs tested for their performance by in silico PCR. 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).

Additional file 3.

List of the seven most promising primer pairs for biodiversity assessments identified by in silico PCR. Primer pairs are suitable for different sequencing methods dependent on the expected amplicon size. Sequence coverage rate of diverse fungal and non-fungal eukaryotic groups as revealed by in silico PCR.

Additional file 4.

Annealing temperatures empirically evaluated for the most promising primer pairs. Two fungal strains, one of the Basidiomycota and one of the Ascomycota, served as template DNA. Intensity of the color indicates the strength of the amplification product detected by ethidium bromide staining. Red, template DNA from Taphrina deformans; Green, template DNA from Agaricus bisporus; *, optimal annealing temperature.

Additional file 5.

Performance of the most promising primer pairs empirically tested on 12 fungal strains.

Additional file 7.

Primer pairs suitable for the amplification of specific fungal phyla/subphyla. Characteristics of the primer pair and sequence coverage rate of the target group is indicated.

Additional file 8.

List of the designed annealing blocking oligonucleotides for the eukaryotic groups Stramenopiles, Alveolata, Rhizaria and Telonema. Characteristics and sequence coverage rates of fungal and non-fungal eukaryotic groups are given.

Additional file 11.

Taxonomic composition of three environmental samples. Barchart indicates relative sequence abundance of the different fungal classes/subgroups amplified by the primer pair nu-SSU-1334-5′/nu-SSU-1648-3′ (FF390/FR-1). Others: Blastocladiomyetes, Glomeromycetes, Monoblepharidomycetes, Pucciniomycotina_Incertae sedis.

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Banos, S., Lentendu, G., Kopf, A. et al. Correction to: A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol 19, 249 (2019). https://doi.org/10.1186/s12866-019-1628-y

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