Sequencing of chromosome ends and characterization of a telomere-linked helicase gene family in the rice blast fungus Magnaporthe oryzae

In many eukaryotic microbes, subtelomeres harbor large gene families with important roles in niche exploitation. Frequent recombination in these locations is believed to produce the variation that fuels adaptation. Subtelomeric regions in Magnaporthe oryzae are known to contain avirulence genes, suggesting that telomere-associated genes may contribute to pathogenic adaptation in this fungus. Telomeres and their associated sequences are underrepresented in the Magnaporthe oryzae whole genome assembly (V.2). To correct this deficiency, I developed a data mining strategy to identify telomere-containing clones from the Magnaporthe Sequencing Project, which I then sequenced to completion and mapped to the whole genome assembly. The most terminal portion of the M. oryzae chromosomes exhibit a significant level of genetic redundancy; 11 of 14 chromosome ends share a core sequence consisting of a single telomere-linked helicase (TLH) gene flanked by varying numbers of short repeats. This core sequence is truncated at various positions in most chromosome ends by 20-30 iterations of the telomere repeat array (TTAGGG)n. Centromere-proximal repeats define the core sequence border with chromosome-unique sequence, indicating that they may have a functional role in the spread of TLH sequences to chromosome ends, possibly as part of an end-maintenance strategy. M. oryzae subtelomeres are enriched in full-length and truncated transposable elements, although none of these are exclusively associated with chromosome ends. These repetitive sequences, in addition to the rDNA array at one chromosome end, were associated with de novo telomeres that arose during culture of the sequenced strain. In contrast to other pathogenic microbes characterized to date, the M. oryzae subtelomeric regions are devoid of large gene families, with the exception of the TLH genes. I performed an in silico analysis of other fungal genome assemblies which revealed that TLH gene families are a frequent component of the distal subtelomeric domains of ascomycete and basidiomycete fungi. My analysis of predicted TLH protein sequences supports previous predictions that TLH genes likely encode RecQ helicase proteins. I also identified a novel domain and DNA-binding motifs that are conserved upstream of the RecQ helicase motifs of predicted TLH proteins, distinguishing TLH proteins as a distinct RecQ subfamily.