The translation elongation factor 1-alpha gene is very specific to specification Fusarium spp, Can I use the translation elongation factor 1-alpha gene to speciation other fungal species.
An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes.
A J Roger, O Sandblom, W F Doolittle and H Philippe Mol Biol Evol (1999) 16 (2): 218-233.:
"EF-1 alpha is a highly conserved protein suggested to have desirable properties for phylogenetic inference. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent.
Overall, the results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. "
I have good experience with EF-1 alpha in taxonomy of some members of Helotiales and Pezizales. However, be aware that EF-1 alpha contains introns (I identified 1-3 introns depending on fungal species and the primer pair used, i. e. 983F/2218R) and they may cause troubles in alignments and phylogenetic analyses.
Maybe, also this study, although designed for zygomycetes, is of some help for you:
Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF-1alpha genes.K Voigt, J Wöstemeyer
ABSTRACT: True fungi (Eumycota) are heterotrophic eukaryotic microorganisms encompassing ascomycetes, basidiomycetes, chytridiomycetes and zygomycetes. The natural systematics of the latter group, Zygomycota, are very poorly understood due to the lack of distinguishing morphological characters. We have determined sequences for the nuclear-encoded genes actin (act) from 82 zygomycetes representing all 54 currently recognized genera from the two zygomycetous orders Mucorales and Mortierellales. We also determined sequences for translation elongation factor EF-1alpha (tef) from 16 zygomycetes (total of 96,837 bp). Phylogenetic analysis in the context of available sequence data (total 2,062 nucleotide positions per species) revealed that current classification schemes for the mucoralean fungi are highly unnatural at the family and, to a large extent, at the genus level. The data clearly indicate a deep, ancient and distinct dichotomy of the orders Mucorales and Mortierellales, which are recognized only in some zygomycete systems. Yet at the same time the data show that two genera - Umbelopsis and Micromucor - previously placed within the Mortierellales on the basis of their weakly developed columella (a morphological structure of the sporangiophore well-developed within all Mucorales) are in fact members of the Mucorales. Phylogenetic analyses of the encoded amino acid sequences in the context of homologues from eukaryotes and archaebacterial outgroups indicate that the Eumycota studied here are a natural group but provide little or no support for the monophyly of either zygomycetes, ascomycetes or basidiomycetes. The data clearly indicate that a complete revision of zygomycete natural systematics is necessary.
Gene 06/2001; 270(1-2):113-20
We have observed that even the short intron region of elongation factor 1-alpha can be successfully used to resolve complex problems in Diaporthe (Phomopsis). Also it can be true about the difficulties of getting better global alignments of intron regions in highly diversified genera, but this may not a problem regarding species complexes in fungi. http://link.springer.com/article/10.1007%2Fs13225-014-0297-2