Molecular phylogeny and RNA secondary structure of Fusarium species with different lifestyles

Abstract

The definition of endophytes ranges from symbiotic to balanced antagonism and/or latent plant pathogens. This indicates a close affiliation between endophytes and pathogens but molecular evidence confirming these relationships are still to be elucidated. We investigated the relationship of endophytic, saprobic and pathogenic Fusarium species as a model genus based on ITS sequences and ITS2 secondary structure analysis. Altogether 212 Fusarium species mostly named in GenBank with ranging lifestyles were used in this study. Species deposited in GenBank were found to be often wrongly named based on sequence comparison as species with the same names were polyphyletic, while differently named species often had the same sequences. Phylogenetic analysis by three different methods (UPGMA, NJ and MP) revealed that similar named species clustered together, but did not form well distinct clades reflective of their lifestyles. Several species were polyphyletic, while several other unrelated species appear to share the same ITS sequences. Since ITS rDNA sequence based phylogeny did not showed distinct relationships, ITS2 consensus secondary structures were used. Endophytes showed close molecular structural affinity with pathogens but structural features of saprobes was very different. Although care must be taken when using sequences from named Fusarium species in GenBank this study provides molecular evidence that endophytes share a close relationship with pathogens and agrees with the assumption that endophytes are latent pathogens.

A novel echinocandin MIG0310 with anticandida activity from newly isolated Fusarium sp. strain MS-R1

“…The strain was identified by sequencing the internal transcribed spacer (ITS) region of the rRNA basically according Barik et al (2011). Briefly, genomic DNA was extracted from dry pulverized mycelium by phenol/chloroform procedure (Henrion et al 1994).…”