Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies

LINE-1 mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data or human cohorts mostly relied on detecting discordant mappings of paired-end short reads, or assumed L1 hallmarks such as polyA tails and target site duplications. Moreover, there has been few genome-wide comparison between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate approach to the discovery of processed pseudogene. Our method utilizes long read assemblies, and more importantly, is able to provide full retrocopy sequences as well as the neighboring sequences which are missed by short-read based methods reads. We provided an overview of novel gene retrocopies of 40 events (38 parent genes) in 20 human assemblies, a significantly higher discovery rate than previous reports (39 events of 36 parent genes out of 939 individuals). We also performed comprehensive analysis of lineage specific retrocopies in chimpanzee, gorilla and orangutan genomes.