Sequences of Assembled Telomere Arrays Record the History of Events on the Ends of Chromosomes

Because telomere arrays are formed by successive transpositions of retrotransposons, each element is younger than its proximal neighbor and the distal 5’ end of each element is at risk of terminal erosion until another element transposes to protect it. Unfortunately, this historical information is difficult to obtain because the complex repeated sequences in telomere arrays preclude accurate assembly by whole genome sequencing. We have collaborated with the Drosophila Heterochromatin Genome Project to do directed assembly of >70kb (kilobases) of telomere array from D. melanogaster chromosome 4R and >20kb from chromosome XL. Neither sequence reaches the chromosome terminus but each is linked to subtelomere sequence and therefore contains the oldest elements in its array. Both arrays are composed entirely of HeT-A and TART elements, each with its 5’ end toward the end of the chromosome, as expected if they were reverse-transcribed onto the 3’OH on the end of chromosomal DNA. Many of the retrotransposons are 5’-truncated, some severely, but none show other evidence of sequence decay. It is not obvious that these elements would be under selection for continued functionality after they enter the array but, except for 5’-truncation, even the oldest members retain the sequences we believe necessary for transposition. Surprisingly, there is a good proportion of intact, unmutated, elements.