Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

Abstract

Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.

Identification and characterization of retro-DNAs, a new type of retrotransposons originated from DNA transposons, in primate genomes

“…There have been very few, if any, published reports for lineage-specific or species-specific DNA transposons in primate genomes. However, in our recent comparative analysis of species-specific MEs in eight primates from the Hominidae and the Cercopithecidae families, in addition to the identification of 228,450 species-specific retrotransposons (Tang and Liang 2019), we also identified a total of 2,405 DNA transposons which are also species-specific that were not included in our report. As part of efforts to understand the mechanisms underlying these species-specific DNA transposons, we report in this study a new type of non-LTR retrotransposons derived from DNA transposons.…”

“…For example, between the human and chimpanzee pair, the chimpanzee genome has more than 10% of da-DNAs than the human genome (28,273 vs. 25,933), while between the two macaques, the rhesus genome has ~10% more than the crab-eating macaque genome (28,149 vs. 26,218) (Table 1). Interestingly, this difference is much less than that for the species-specific non-LTRs, which shows crab-eating macaque genome having a much lower retrotransposition activity than the rhesus genome (Tang and Liang 2019). This may indicate that majority of these da-DNAs were generated by a mechanism different from retrotransposition.…”

“…In this study, we chose to use ten primate genomes including human, among which eight genomes were inluded in our previous study for identifying species-specific MEs in primates (Tang and Liang 2019…”

“…These files contain the information linking the orthologous positions in a pair of genomes based on lastZ alignment (Harris 2007). Twenty-two of these were available and downloaded from the UCSC genome browser site, and another 34 liftOver chain files were generated using a modified version of UCSC pipeline RunLastzChain (http://genome.ucsc.edu) from a previous study (Tang and Liang 2019). The remaining 36 liftOver chain files were newly generated using the same pipeline.…”

“…Mobile elements (MEs), also known as transposable elements, as a whole constitute significant proportions of the genomes for most higher organisms, being around 50% in primate genomes (Carbone et al 2014;Chimpanzee Sequencing and Analysis 2005;Cordaux and Batzer 2009b;Deininger et al 2003;Higashino et al 2012;Lander et al 2001;Locke et al 2011;Rhesus Macaque Genome Sequencing and Analysis et al 2007;Scally et al 2012;Tang and Liang 2019;Warren et al 2015;Yan et al 2011). MEs are defined as genomic sequences capable of changing locations or making copies into other locations within genomes.…”