Analysis of Recent Expansions of Select Retrotransposon Families in Soybean

LTR retrotransposons are the dominant feature of the genomic landscapes of many higher plants. There are hundreds of element families of varying sizes ranging from a few members to thousands. Their impacts on genome structure is patently obvious, but the roles they play in genome function are just now being recognized as non-trivial and dynamic. With the completion of many plant genome sequencing projects, there are now expansive catalogs of LTR retrotransposons that document their distribution and the evolutionary relationships of the many different families. However, few studies have focused on analyzing the expansion of single families within genomes at the level of temporal, structural, and ancestral relationships of individual members. Traditional phylogenetic tree building programs do not accurately reconstruct the ancestry of single families within genomes. We have focused this study on two LTR retrotransposon families in the soybean genome, SIRE1 (also known as Gmr2) and Gmr30. Both families have undergone recent expansion in the last 250,000 years with many possibly functional members. The SIRE1 family is a member of the Ty1/copia-like superfamily with over 800 full-length members. The Gmr30 family is a member of the Ty3/gypsy-like superfamily with at least 63 full-length members. We have used a recently published program to reconstruct the complex ancestral relationships of all members of each family and have superimposed on this network genomic locations, times of insertion, and mutational events of each member. These relationships provide a more precise evaluation of patterns of retrotransposon proliferation and change.