How To Obtain The Ancestral Repeats For Drosophila

Question

[EvoGen]

Hello, Has anyone worked with the ancestral repeats? I am interested in obtaining the ancestral repeat sequences for Drosophila. Can anybody let me the general method or tool or database or resource to obtain ancestral repeats in this species.

Thanks in advance

Answer 1

[Casey Bergman]

I assume you are asking about finding instances of ancestral repeats, not identification of ancestral repeat families themseles. In either case, unlike mammalian genomes, there are very few ancestral repeat families in Drosophila, so the reason there is no database available is because there is very little data of this type for Drosophila. This is mainly a result of the fact that there is a high rate of deletion of unconstrained DNA in Drosophila (see this paper for the original observation). The only TE family that is widely distributed across the D. melanogaster genome and present in other species (like D. simulans) is the INE-1 (aka DINE-1, aka NAREP) family. Since INE-1 is no longer active, the INE-1 copies RepeatMasker identifies are often ancestral, but you can intersect RepeatMasker output with pairwise alignments as Istvan suggests to confirm which instances are actually present in other closely releated species.

On a related note, the flipside of having very few ancestral repeats in Drosophila has been used effectively by Caspi and Pachter to identify new TE instances and families in multiple sequence alignments (paper is here). Very few people have taken advantage of the biology of Drosophila repeats to develop compTE-like methods, and this is currently an open area of research.

Answer 2

[Istvan Albert]

The general method is described in Ancestral repeats pipeline

• collect repeatmasker annotation from external databases.
• build pairwise genomic alignments
• define ancestral repeats
• compute rates of ancestral repeats

[EvoGen]

And how would one exactly define the ancetral repeats in an organism?

[SES]

Just for reference, this general method has been used to reconstruct numerous ancestral TEs. Perhaps most famously, the Sleeping Beauty transposon, which is a synthetic element that will actively transpose in numerous species and is an important molecular tool for mutagenesis.