Plasticity of the subtelomeric TLO gene family via rapid recombination mechanisms

Subtelomeric regions are hotspots of genomic evolution due to increased accumulation of polymorphisms and gene family expansions.  The telomere-associated (TLO) gene family of Candida albicans has undergone a recent expansion within the subtelomeric regions.  The 14 TLO genes fall into three clades: Clade II has a single, unique TLO gene; the majority of TLOs fall within Clades I, which has no intron, or Clade III, which can undergo splicing.  Evidence that TLOs are mobile is based on discordance between the reference genome (SC5314) and the chromosome arms associated with a number of different tagged TLOs.  We followed recent TLO movement events in three independent series of strains in which a unique TLO moved from one chromosome arm to another.   Two of the TLO movement events occurred within a common 49bp sequence immediately proximal to the TLO.  Surprisingly, one event occurred within a TLO open-reading frame, producing a novel, chimeric TLO gene.  All movement events were gene replacements due to non-reciprocal single crossovers, yielding the gain of one copy of the invading TLO and the loss of one copy of the original TLO.  Furthermore, the gain/loss of TLOs affected their levels transcription, either due to copy number variation and/or to the context of the TLO in a new genomic environment.  In summary, the subtelomeric regions of C. albicans are highly plastic and are changing their chromosomal locations and relative composition with a high frequency, thereby altering the repertoire of TLO genes and the degree to which different TLO genes are expressed.