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A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene
Author(s) -
PérezIzquierdo L.,
Morin E.,
Maurice J. P.,
Martin F.,
Rincón A.,
Buée M.
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12678
Subject(s) - biology , phylogenetic tree , gene , genetics , phylogenetics , amplicon , genome , indel , genomic dna , ribosomal rna , polymerase chain reaction , genotype , single nucleotide polymorphism
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer ( ITS ) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel‐induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single‐copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH 63 gene, encoding exo‐acting α‐glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNA s, and GH 63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N ‐acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH 63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH 63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH 63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH 63 and Rpb1 protein sequences revealed that GH 63 is also a promising phylogenetic marker. Finally, a very high proportion of GH 63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.