Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions

Abstract

Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of the SORE-1 family of soybean retrotransposons using genome sequencing data. Insertion time of each SORE-1 element into the genome was estimated on the basis of sequence differences between the 5' and 3' long terminal repeats (LTRs). Combining this estimation with information on the chromosomal location of these elements, we found that the insertion of the existing SORE-1 into gene-rich chromosome arms occurred on average more recently than that into gene-poor pericentromeric regions. In addition, both the number of insertions and the proportion of insertions into chromosome arms profoundly increased after 1 million years ago. Solo LTRs were detected in these regions at a similar frequency, suggesting that elimination of SORE-1 via unequal homologous recombination was unbiased. Taken together, these results suggest the preference of a recent insertion of SORE-1 into chromosome arms comprising euchromatic regions. This notion is contrary to an earlier view deduced from an overall profiling of soybean retrotransposons and suggests that the pattern of chromosomal distribution can be more diverse than previously thought between different families of retrotransposons.

New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species

“…It is worth noting that three families of Copia elements were under positive selection (adaptive molecular evolution) pressure (Figure 7A), and insertion position structure analysis results indicated that these elements integrated mainly within the promoter or gene regions (Figure 8B,C, Figures S7 and S8), introducing some cis -acting regulatory elements to the promotors of genes (Table S1) or playing import roles in the evolution of some genes. As reported in previous studies, Gypsy elements tend to be clustered into the chromosomal centromeric regions [11,17,34], while other studies suggested that Copia elements were largely within and/or close to gene regions [35,36,37]. These results suggested that, of the two-retrotransposon superfamilies, the Copia elements may have the dominant influence on the evolution of some mulberry genes.…”

Distribution and Characteristics of Transposable Elements in the Mulberry Genome

“…Similar phenomena had also been found in soybean [ Glycine max (L.) Merr. ], in which Copia ‐type retrotransposon ( SORE‐1 ) insertions are more recently and frequent in chromosome arms than in pericentromeric regions (Nakashima et al, 2018). A typical example is that it inserted in the first intron of the GmFT2a gene of soybean where it attenuated the expression level of this gene, causing delays in flowering (Zhao et al, 2016).…”

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

“…Due to the "copy and paste" mechanism underlying the amplification of LTR retrotransposons, they have been shown to make up the largest classes of transposable element (TE) content in the genomes of most flowering plants, greatly contributing to increases in size of their host genome [66]. As reported in studies concerning Arabidopsis, soybean, and flax genomes, Copia elements are largely located within and/or close to gene-coding regions, which suggests that these elements may have the dominant influence on the evolution of some gene families [67][68][69]. Gene prediction revealed features characteristic of gene-rich regions, with an average of 13 coding sequences per 100 Mbp for both GS and PEPC gene regions ( Table 1, Supplementary file 1).…”