Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Abstract

BackgroundResearch into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage.ResultsHere we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily.ConclusionsThe retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.

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

“…For example, non-reference retrocopies of PPIA were seen in the human samples and the three great apes, however all inserted to different spots (human at chr4, chimpanzee at chr6, gorilla at chr11 and orangutan at chr5). Retrotransposition activity level of gorilla, measured by lineage-specific Alus, has been reported to be lower than that of humans (McLain et al 2013), possibly explaining the lower number of gene novel retrocopies seen in our gorilla sample; chimpanzee was reported to have significant higher speed of accumulating L1 insertions (Mathews et al 2003), consistent with the observation here. Our results translate to roughly 46 gene retrotransposition events per million years in chimpanzees, 20/my for gorillas and 26/my for orangutans.…”

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

“…The results of this study show an ongoing expansion of Alu elements in the Papio lineage, with more novel recently integrated subfamilies of Alu elements present than in any other previously analyzed human or non-human primate genome [ 15 , 32 , 60 – 68 ]. For comparison, only 14 lineage-specific Alu subfamilies were found in the genome of the rhesus macaque [ 61 ], and 46 Saimiri- specific Alu subfamilies were found in a recent analysis [ 32 ].…”

“…These major subfamilies of Alu elements can be further expanded based on diagnostic mutations that they have accrued over millions of years [ 31 ]. Some subfamilies of elements can be shared within a number of closely related taxa, but other recent studies have identified elements that are unique to only a particular species or genus [ 15 , 32 ]. This parallel evolution of Alu subfamilies results in each primate lineage having its own network of recently integrated Alu subfamilies [ 2 ].…”

Can-SINE dynamics in the giant panda and three other Caniformia genomes

“…An age estimate for each subfamily was determined by an average of results based on the two types of mutations (CpG and non-CpG mutations) with a custom Perl script [ 54 ]. For the second method, the BEAST program, applied to estimate dates of divergence using transposon data previously published [ 55 , 56 ], was used to estimate the age of the PPS_SINEC1_AMes and PPS_SINEC1B_AMes elements with the following parameters: Site Heterogeneity = ‘gamma’; Clock = ‘strict clock’; Species Tree Prior = ‘Yule Process’; Prior for tmrca = ‘Normal distribution’ with 2.0 standard deviation; Prior for clock.rate = ‘Uniform’ with initial rate set at 0.0013 (neutral mutation rate) and upper rate set at 0.0104 (CpG mutation rate) to include the major mutation rates found in the panda genome. All other parameters were set at default settings.…”