Insights into mammalian TE diversity through the curation of 248 genome assemblies

Abstract

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.

Fig. 1.. Correlation of total genomic TE content and the size, in base pairs, of the genome.

Because of the log transformation and scaling of assembly size for the hierarchical Bayesian analysis and the resulting back-transformation, the x-axis values are approximately rendered. The blue line indicates the line of best-fit, and the shaded area is the 95% high probability density of the fit. The R² for this relationship was estimated at 0.54 (95% high probability density, 0.42 to 0.64).

Fig. 2.. Total and young TE genomic proportions by species within a phylogenetic context.

Dots at branch tips indicate the TE class most prevalent among recent TE insertions (insertions with <4% divergence from the relevant consensus TE). The ring immediately following the branch tip dots indicates the mammalian order for each respective species. Orders represented by numbers are as follows: 1, Cingulata; 2, Pilosa; 3, Sirenia; 4, Proboscidea; 5, Hyracoidea; 6, Macroscelidea; 7, Tubulidentata; 8, Afrosoricida; 9, Scandentia; 10, Dermoptera; 11, Lagomorpha; 12, Eulipotyphla; 13, Perissodactyla; and 14, Pholidota. The inner ring of stacked-bar data depicts the total percentage of the genome attributed to the five main categories of TEs: DNA transposons, LINEs, SINEs, LTRs, and rolling circle transposons. The outer ring of stacked-bar data shows the percentage of the genome derived from recently inserted TEs. Cladogram adapted from (65).

Fig. 3.. Redundancy analyses examining major axes of variation in TE accumulation and genome size related to orders and families of mammals.

Arrows represent significant correlations of TE types with the first two RDA axes. Each axis reflects changes in TE composition related to ordinal (top) or familial (bottom) affiliation of taxa used in analyses. Gray circles represent orders or families that were not significantly correlated to at least one of the RDA axes, whereas black circles represent orders or families with significant correlations.

Fig. 4.. Stacked bar charts depicting proportions of recently accumulated TEs (<4% kimura divergence from consensus TE) in bats.

Data are organized by TE classification and plotted onto the tips of the chiropteran portion of the mammalian tree, adapted from (65).

Fig. 5.. Recent mammalian TE diversity in relation to Shannon H and Pielou’s J.

The blue lines indicate the lines of best-fit, and the shaded areas are the 95% high probability density of the fit. The R² for H (left) was estimated at 0.67 (95% high probability density, 0.52 to 0.78), and for J (right), the R² was 0.69 (95% high probability density, 0.56 to 0.79).

Fig. 6.. Half eye plots depicting fold differences in recent DNA transposon accumulation among three dietary phenotypes: carnivore, herbivore, and omnivore.

Instead of showing the estimated values for each of the diets, these plots depict the fold ratio between each diet pair, so that the plot itself shows statistical significance. Comparisons for which the thin line does not overlap with 1 are significant (indicated by asterisks). Plots correspond to the following taxonomic groups: (A) placental mammals [R² estimated at 0.92 (95% high probability density, 0.79 to 0.97)], (B) Artiodactyla [R² estimated at 0.64 (95% high probability density, 0.32 to 0.78)], (C) Chiroptera [R² estimated at 0.34 (95% high probability density, 0.02 to 0.86)], (D) Primates [R² estimated at 0.18 (95% high probability density, 0.00 to 0.58)], and (E) Rodentia [R² estimated at 0.07 (95% high probability density, 0.00 to 0.28)].