Do you have an idea how to get subtelomeric and telomeric regions of the newly sequenced organism? I have got fungal species assembly with >50x coverage and closely related genomes already sequenced.
Cheers,
Telomeric regions consists of highly repetitive chunks of sequence, they shouldn't be in the assembly after all, but try RepeatMasker or Dust to detect such low-complexity regions in the assembly.
I read a paper about synteny...they also talk about assembly of related genomes and transciptomes....maybe this helps to compare your newly sequenced organism with the related ones by their synteny..?? just an idea....
Have a look: http://genomebiology.com/2011/12/5/R45
Cheers Steve
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Sorry, but syntheny has nothing to do with telomeres (telomeres always located at the 'ends' of the chromosme), just throwing in some random answers?
In some cases if the organism are closely related their is syntheny of genes, also of genes which are nearly located to telomeric regions....i thought of taking these genes as a marker which might gives you a hint for telomeric regions in their up/downstream regions......