Replication of Nonautonomous Retroelements in Soybean Appears to Be Both Recent and Common  

Abstract

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.Transposable elements are abundant components of plant genomes. They are typically divided into two groups based on their mechanism of transposition. Class I transposons transpose via an RNA intermediate and must therefore use reverse transcriptase (RT) during the replication process. Class II transposons do not have an RNA intermediate and usually use a cut-andpaste mechanism for transposition . Elements of both classes have had major impacts on genome structure, apparently not only promoting mutations of genes and affecting gene regulatory sequences but also playing a substantial role in the creation of new genes by "exon-shuffling" and retrotransposition (Jin and

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean

“…However, the precise locations of retroelement insertions in G. tomentella differ from those in soybean, with the distances between any two low-copy genes varying substantially between these two species. Consistent with this, many of the retroelements in G. tomentella have intact LTRs and represent insertions that occurred within the last 4 million years (Wawrzynski et al, 2008), after the split between G. tomentella and soybean. Although older insertions are almost certainly present, they are difficult to detect due to the degradation of LTR sequences caused by insertions and deletions.…”

“…1). A diverse collection of retroelements was found in H2 of both soybean and G. tomentella, including copia-like and gypsy-like long terminal repeat (LTR) retrotransposons, as well as LINE elements (Wawrzynski et al, 2008). The majority of the LTR retroelements identified in both soybean and G. tomentella, however, inserted within the last 4 million years, and many within the last 1 million years (Wawrzynski et al, 2008).…”

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

“…For other soybean homoeologous regions, excluding pericentromeric regions, it was 7.8 LTR retrotransposons/Mb (Wawrzynski et al, 2008). In addition, Gm15 had higher densities of other classes of LTR retrotransposons than Gm8, for instance, fragmented LTR retrotransposons (truncated and remnants of LTR retrotransposons) and total LTR retrotransposons from all classes.…”

Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

“…The ratio of intact elements to solo LTRs fluctuates greatly between retrotransposons in different plant species-from $8:1 (eight intact elements to one solo LTR) in soybean (Wawrzynski et al 2008), implying very slow rates of TE sequence removal, to $1:9 (one intact element to nine solo LTRs) for LARD retrotransposons in barley, probably due to abundant homologous recombination events (Kalendar et al 2004). Our estimation of the genomic distribution of Veju elements showed that the genomes of the parental lines TTR19 and TQ27 possessed as many as 2.7 to 6.8 times more LTRs, respectively, than intact Veju elements.…”