Characterization of Chromosome Ends in the Filamentous FungusNeurospora crassa

Abstract

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.

Basidiomycetes Telomeres – A Bioinformatics Approach

“…This approach allowed our group to map 19 out of the 22 chromosome ends expected in its linkage map (Perez et al, 2009), as well as to study the telomere adjacent regions. Similar strategies have been described by different authors (Rehmeyer et al, 2006;Sanchez-Alonso & Guzman, 2008;Wu et al, 2009). The search for telomere regions was performed in whole genome sequence draft assemblies.…”

“…This sequence has been described in Aspergillus nidulans (Bhattacharyya & Blackburn, 1997), Beauveria bassiana (Padmavathi et al, 2003), Botrytis cinerea (Levis et al, 1997), Cladosporium fulvum (Coleman et al, 1993), Fusarium oxysporum (Inglis et al, 2000), Glomus intraradices (Hijri et al, 2007), Magnaporthe grisea (Gao et al, 2002), Metarrhizium anisopliae (Inglis et al, 2005), N. crassa (Wu et al, 2009), Pestalotiopsis microspora (Long et al, 1998), Pleurotus ostreatus (Perez et al, 2009), Pneumocystis carinii (Keely et al, 2001), and Ustilago maydis (Sanchez-Alonso & Guzman, 2008). However, variations of this sequence can be found in other fungi such as A. oryzae that has dodecanucleotide telomere repeats (Kusumoto et al, 2003) Incomplete and imperfect telomere units have been reported in: A. oryzae, Candida albicans, Kluyveromyces lactis, S. cerevisiae and S. pombe.…”

“…In humans, there are more re-arrangements at the sub-telomere regions than in the rest of the genome. This is also true in some lower eukaryotes such as Plasmodium falciparum (FreitasJunior et al, 2000), Magnaporthe oryzae (Rehmeyer et al, 2006) and Neurospora crassa (Wu et al, 2009), among others. In all these cases genes involved in niche adaptation (species-specific genes) were found in the subtelomeric regions.…”

“…A similar situation was reported in P. falciparum and Trypanosoma brucei where families of antigen surface proteins inducing immune responses are encoded in telomere regions as part of a pathogen's mechanism to amplify and diversify surface antigen genes to avoid host recognition, as it has been hypothesized (Barry et al, 2003). To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, Farman's group analyzed and characterized the telomere organization in the rice blast pathogen M. oryzae (Rehmeyer et al, 2006) and in N. crassa (Wu et al, 2009). The molecular and bioinformatics approach allowed them to identify 14 chromosomes in both of them.…”

“…The identified protein sequences were also used to query the online Pfam database using default parameters (Bateman et al, 2004). A similar approach has also been used by Wu et al (2009) to search for subtelomere regions containing gene in N. crassa. This type of multiple analysis (genetic, molecular, and bioinformatics) allows the characterization of most of the P. ostreatus telomeres as well as several subtelomere regions that show high nucleotide similarity.…”