Genome-Wide Characterization of Nonreference
Evolutionary Propensities of Transposons in Soybean
Transposons
Reveals
Preferential accumulation of transposable elements (TEs), particularly long terminal
repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric
regions seems to be a general pattern of TE distribution in flowering plants. However,
whether such a pattern was formed primarily by preferential TE insertions into
pericentromeric regions or by selection against TE insertions into euchromatin
remains obscure. We recently investigated TE insertions in 31 resequenced wild and
cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference
TE insertions mappable to the reference genome. Our data revealed consistent
distribution patterns of the nonreference LTR-RT insertions and those present in the
reference genome, whereas the distribution patterns of the nonreference DNA TE
insertions and the accumulated ones were significantly different. The densities of the
nonreference LTR-RT insertions were found to negatively correlate with the rates of
local genetic recombination, but no significant correlation between the densities of
nonreference DNA TE insertions and the rates of local genetic recombination was
detected. These observations suggest that distinct insertional preferences were
primary factors that resulted in different levels of effectiveness of purifying selection,
perhaps as an effect of local genomic features, such as recombination rates and gene
densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in
soybean.