Transposable Element Subfamily Annotation is Unreliable in Biological Replicates

Background: Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that in some cases capture family history, and in other cases are simply intended to improve annotation sensitivity. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee.