Mycobiont-specific primers for lichenized fungal genus Cladonia (Cladoniaceae, Ascomycota)

By

Biwersi, Maia
Xu, Maonian
Heiðmarsson, Starri
Pálsson, Snæbjörn
Sorensen, John L.
Ólafsdóttir, Elín S.

Type

Article

Date of Publication

2026-1-6

Original Publication

MycoKeys

Volume

127

Pages

1--23

Subjects

Cladonia , Cladoniaceae , MCM7 , mtSSU , nrITS , PCR , primer design , rpb2

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers 2011-

Identifiers

DOI: https://doi.org/10.3897/mycokeys.127.167091

 

Abstract

<br> Phylogenetic studies in lichenized fungi need reliable primers, as off-target amplification of environmental fungi or the lichen photobiont presents a challenge. In this study, new mycobiont-specific primers were developed and evaluated for four genetic markers (nrITS,<br> RPB2<br> ,<br> MCM7<br> , and mtSSU) within the diverse genus<br> Cladonia<br> . A dataset of 110 specimens was used to assess amplification success, sequence quality, and taxonomic resolution. All markers showed high PCR success rates, with nrITS,<br> MCM7<br> , and mtSSU primer pairs exceeding 90%. nrITS displayed the highest sequence variability and nucleotide diversity, whereas mtSSU was the most conserved. Pairwise genetic distance analyses revealed that nrITS provided the strongest species-level resolution,<br> RPB2<br> offered intermediate divergence,<br> MCM7<br> was informative at the clade level but limited for closely related subclades, and mtSSU was best suited for deeper phylogenetic splits. This study shows the value of targeted primer design, and the new primers proved to be robust tools for future molecular identification and evolutionary research in<br> Cladonia<br> .<br>