BackgroundTransposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production.ResultsWe analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations.ConclusionsThis study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3454-z) contains supplementary material, which is available to authorized users.

An integrated strategy for complete lignocellulose saccharification to maximize bioethanol yield under a cost-effective and green-like biomass process in rapeseed stalk.

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Glucose converted from a diet has been considered a high risk factor of type 2 diabetes mellitus (T2DM). However, it is not clear how it increases the risk of T2DM. Here, we investigated the effect of high glucose administration on glucose tolerence in wild type and toll like receptor 4 (TLR4) knockout mice. Mice were intragastrically administered with high glucose. The level of fasting blood glucose, insulin and intraperitoneal glucose tolerance were measured, and insulinogenic index and HOMA IR were calculated at 1 week. To understand mechanism of glucose action, we also assessed blood glucose, glucagon like peptide 1 and inflammatory cytokines levels at different time windows following high glucose load. Our results show that 20 g/kg glucose load leads to glucose tolerance impairment and insulin resistance in wild type mice. Following 20 g/kg glucose load, the levels of plasma interlukin 6 (IL 6) and tumor necrosis factor α (TNF α) increased significantly in wild type mice, but not in TLR4 knockout mice. Moreover, 20 g/kg glucose load also impaired glucose induced GLP 1 secretion in wild type and TLR4 knockout mice. Our results indicate that high glucose load leads to glucose intolerance with insulin resistance through impairment of GLP 1 secretion, increase of blood glucose levels via activating TLR4 and increasing levels of IL 6 and TNF α in mice.