Information regarding antigen specificity, species of origin, method of cloning, and other relevant serological properties was correlated with the sequence data.
Clonal diversity can originate in at least three different ways [ 53]: 1) through separate and recurrent origin of clones from a sexual ancestor, 2) through hybridization between asexual females with males (either from the same or from other species), or 3) through mutation.
Origin of clones: BS bulk soil, ROOT rhizosphere, VM volcanic mud, WW waste water sludge, RV bioreactor enrichment from vercelli, RS Methylacidiphilum fumariolicum SolV, DAMO Methylomirabilis oxyfera enrichment culture.
We acknowledge that this first model does not include the full complexity of our design, as it ignores the origin of clones and strains in the analysis (but see below for an analysis that does take origin into account).
Indeed, the ability to detect the polyphyletic origin of clones depends not only on true clonal diversity but also on the variability of applied markers and the ancestral sexual population as well as sampling design (see [ 27, 28] for review).
This technique allows positive confirmation of the origin of genes cloned from obligate pathogenic fungi and could be adapted for use on any samples containing mixed fungal species.
These are pRS313-based plasmids containing the SV40 origin of replication cloned into the ApaI site.
Additional file 6: Table S1 outlines the origin of the cloned genes and the carbohydrases that they encode.
