CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES
Location: Corn Insects and Crop Genetics Research
Title: Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison
| Du, Jianchang - |
| Tian, Shixi - |
| Hans, Christian - |
| Jackson, Scott - |
| Shoemaker, Randy |
| Ma, Jianxin - |
Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 15, 2010
Publication Date: June 16, 2010
Citation: Du, J., Tian, S., Hans, C., Jackson, S., Cannon, S.B., Shoemaker, R.C., Ma, J. 2010. Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant Journal. 63(4):584-598.
Interpretive Summary: The organization and structure of flowering plant chromosomes is often quite complex. Scientists have collected evidence regarding the evolutionary relationships of many plant species. However, much of this information is based on physical attributes of the plants. What is lacking is an indepth analysis of those elements of chromosomes that are known to modify chromosome structure. In this paper, the authors take advantage of the recently completed decoding of all of the soybean DNA to analyze elements known as 'jumping genes'. They show that some of the elements can be traced through evolutionary lineages back to a time before grasses separated from non-grass species, about 100 million years ago. This gives scientists more insight into how complex genomes came about and how they have come to have common features, even among distantly related species. This information is important for the better understanding of plant evolution.
The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 LTR-retrotransposon (LTR-RT) families that are comprised of 32,370 elements in soybean. Approximately 87% of these elements were located in recombination-suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that (1.62) of chromosome arms. Further analysis revealed a significant positive association between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed 7 Copia-like and 5 Gypsy-like evolutionary lineages that had existed before the divergence of dicot (e.g., Arabidopsis) and monocot species (e.g., rice), but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, one of the 7 Copia-like lineage has been lost in soybean. Analysis of physical association of LTR-RTs with centromere satellite repeats identified two putative centromere retrotransposon families of soybean (CRS), which were grouped into the CR (e.g., CRR and CRM) lineage of grasses, indicating that the functional specification of CR predate the bifurcation of dicots and monocots. However, a number of families of the CR lineage are not physically associated with centromeres, suggesting that their CR roles may have been defunct. Our data also suggest that the putative Copia retrovirus-like family, SIRE, is likely derived from the Gypsy retrovirus-like Athila lineage, and thus we propose a hypothesis of the single ancient origin of retrovirus-like elements in flowering plants.