Transposable Activity And True Application Of A Class Of Tiny Inverted Inverted Transposable Elements (MITE) In The Tobacco Genome

Miniature inverted-repeat transposable element (MITE) is the most abundant DNA element identified in plants genome and involved in many important biological events. However, only few of the MITE families are confirmed as active transposable elements, which makes it very challenging to study its mechanism. In this study, we aimed to enhance our understanding of MITE transposition in tobacco (Nicotiana tabacum) plants. Bioinformatics analytical tools, such as MITE-Hunter, Muscle-Multiple Sequence Alignment and TIR/TSD analysis, were employed to study MITE sequence structural features and copy numbers of tobacco genes from the NCSU database. From almost 2 million publicly available tobacco gene sequences, we were able to reveal 21 different MITE family (named TMi 1 to TMi 21), in which,17 of them were reported for the first time in this study and 4 of them were recently reported by other researchers. Amongst all of the newly identified MITE family, we were particularly interested in TMi 1 family. Identification of TMi 1 element polymorphism in different tobacco strains had provided preliminary evidence of MITE transposition activity. Moreover, we had established 2 specific biological phenotypes for transposon display assay and the results showed that TMi 1 was an active transposon element. This was the first time which an active MITE was reported in tobacco genome. For the last 2 decades, MITE and its transposition activities were studied mainly in rice (Oryza sativa) plant models. This study not only identified new MITE family, but also validated that tobacco plant was a very useful tool for studying MITE and its transposition activities. We demonstrated that tobacco genome was a transposon-rich species and potentially possess novel active MITE elements. Such discovery provides new perspectives and improves our understanding in MITE transposon and gene regulation. Therefore, further investigation of MITE activity in tobacco plants is required and possibly will re-define the principal of genome evolution and genetic biodiversity formation. Molecular marker genetic linkage map is the basis of gene mapping, positional cloning and molecular marker-assisted selection breeding. However, the largre common tobacco genome and low level of molecular marker polymorphism make great trouble in research of genetic linkage map construction and gene targeting. Since MITE is characterized by high copy number and prefering to insert into adjacent gene locus, it can be used as an ideal molecular marker. In this study, we detected four strains showing marked DNA polymorphism (respectively PVH19, Yunyan 96, Yunyan 100, Yunyan 108) among nine examined tobacco cultivars. It meant that MITE element was able to construct a high-density genetic linkage map for resistant gene mapping, and then we could identify and filter the resistance genes at the molecular level, which would help to improve breeding efficiency.