|Tian, Zhixi - Purdue University|
|She, Maoyun - Purdue University|
|Zhao, Meixis - Purdue University|
|Du, Jianchang - Academy Of Agricultural Science|
|Liu, Xin - Ministry Of Agriculture - China|
|Xu, Xun - Ministry Of Agriculture - China|
|Lam, Hon-ming - The Chinese University Of Hong Kong (CUHK)|
|Ma, Jianxin - Purdue University|
Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/30/2012
Publication Date: 11/21/2012
Citation: Tian, Z., She, M., Zhao, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Lam, H., Ma, J. 2012. Genome-Wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. The Plant Cell. 24(11): 4422-4436.
Interpretive Summary: The chromosomes of any higher organism, from plants to humans, are comprised of both genes (which carry information about how to build all proteins and enzymes in a cell) and non-genic DNA (some of which has regulatory functions, and some has unknown or no apparent function). The non-genic DNA is usually much more abundant in chromosomes than the genic portion, and is usually comprised mostly of a class of DNA features called "transposable elements" (TEs). Plant geneticists have sought to understand TEs because of their abundance, and because of the capacity of TEs to make copies of themselves and thereby change the structure of chromosomes. TEs also occasionally insert into genes, so they can be an important source of changes and differences between varieties of plants and animals. This study examined TEs in the soybean genome (the set of all chromosomes in a cell) to determine how this important type of DNA is perpetuated in the genome, and how and why it is organized in particular ways in chromosomes. By examining the nearly complete genome sequences from 31 wild and cultivated soybean varieties, this study found that the most common sub-class of TEs copy themselves from one region in the genome, and then re-insert mostly near the centers of chromosomes; and also that near the chromosome centers, TEs are less frequently eliminated from chromosome centers than from nearer the chromosome ends. A different sub-class of TEs has different behavior, copying and re-inserting throughout the genome. These findings help explain large differences in the observed locations of various types of TEs in the soybean -- and in turn, may help plant breeders understand the diversity of the genomes of soybeans and other species, and develop improved crop varieties.
Technical Abstract: Preferential accumulation of transposable elements (TEs), particularly LTR-retrotransposons (LTR-RTs) in recombination-suppressed pericentromeric regions, seems to be a general pattern of TE distribution in many flowering plants. However, whether such a pattern occurs primarily by preferential insertions into the pericentromeres or by selection against insertions of TEs into the euchromatin has been unknown. We investigated TE insertions in 31 resequenced wild and cultivated soybean genomes and detected 34,152 unique TE insertions that are not present in the soybean reference genome sequence. The majority of these non-reference TE insertions were found in single accessions, suggesting their recent occurrence. Profiling of these insertions against the soybean reference genome revealed a consistent distribution pattern of the non-reference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the non-reference DNA TE insertions and the accumulated DNA TEs were significantly different. The density of the non-reference LTR-RT insertions was found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the density of the non-reference DNA TE insertions and the rates of local genetic recombination was detected. Together, these observations suggest that, although purifying selection plays an important role in purging TE DNA from the host genome, distinct insertional preferences are primary factors that lay foundations for different distribution patterns of LTR-RTs and DNA TEs in the soybean genomes.