Platyrrhine Genome Alu Content Analysis

Four high-quality platyrrhine genomes (common marmoset; C. jacchus [caljac3], capuchin monkey; Cebus imitator [Cebus_imitator-1.0], squirrel monkey; S. boliviensis [SaiBol1] and owl monkey; Aotus nancymaae [Anan_2.0]) were obtained from the National Center for Biotechnology Information (NCBI) and analyzed for their Alu content using RepeatMasker (RepeatMasker-Open-4.0). Ascertainment of lineage-specific or recently integrated Alu insertions from the owl monkey genome [Anan_2.0] and from the C. imitator genome [Cebus_imitator-1.0] [25 (link)] were performed as described previously [26 ,27 (link),28 (link),29 (link)]. Briefly, full-length Alu elements were extracted from the RepeatMasker output using a custom python script (described at link https://github.com/t-beck; accessed on 19 December 2022). These elements, along with 600 bp 5′ and 3′ flanking sequence, were then compared to the remaining genomes by means of a sequential BLAT [23 (link)] conducted in the following order: (1) human (Homo sapiens; [GRCh38.p13]); (2) common marmoset (C. jacchus; [caljac3]); (3) capuchin monkey (C. imitator; [Cebus_imitator-1.0] or owl monkey (A. nancymaae; [Anan_2.0] and (4) squirrel monkey (S. boliviensis; [SaiBol1.0]). A sequential BLAT involved analyzing the output after each BLAT for capuchin or owl monkey-specific Alu elements compared to the other four genomes.