Originally published as Genetics Published Articles Ahead of Print on December 22, 2008.

Genetics, Vol. 181, 1129-1145, March 2009, Copyright © 2009
doi:10.1534/genetics.107.084392

Characterization of Chromosome Ends in the Filamentous Fungus Neurospora crassa

Cheng Wu^*,1, Yun-Sik Kim^,2, Kristina M. Smith^,3, Weixi Li^,4, Heather M. Hood^*, Chuck Staben^,5, Eric U. Selker, Matthew S. Sachs^*,**,1 and Mark L. Farman^,6

^* Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, Oregon 97006, Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, Department of Biology, University of Kentucky, Lexington, Kentucky 40506, ^** Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97201 and Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546

⁶ Corresponding author: Department of Plant Pathology, University of Kentucky, Lexington, KY 40546.
E-mail: farman{at}email.uky.edu

Telomeres and subtelomere regions have vital roles in cellular homeostasis and can facilitate niche adaptation. However, information on telomere/subtelomere structure is still limited to a small number of organisms. Prior to initiation of this project, the Neurospora crassa genome assembly contained only 3 of the 14 telomeres. The missing telomeres were identified through bioinformatic mining of raw sequence data from the genome project and from clones in new cosmid and plasmid libraries. Their chromosomal locations were assigned on the basis of paired-end read information and/or by RFLP mapping. One telomere is attached to the ribosomal repeat array. The remaining chromosome ends have atypical structures in that they lack distinct subtelomere domains or other sequence features that are associated with telomeres in other organisms. Many of the chromosome ends terminate in highly AT-rich sequences that appear to be products of repeat-induced point mutation, although most are not currently repeated sequences. Several chromosome termini in the standard Oak Ridge wild-type strain were compared to their counterparts in an exotic wild type, Mauriceville. This revealed that the sequences immediately adjacent to the telomeres are usually genome specific. Finally, despite the absence of many features typically found in the telomere regions of other organisms, the Neurospora chromosome termini still retain the dynamic nature that is characteristic of chromosome ends.

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