Identification of Miniature Inverted-Repeat Transposable Elements and Development of Molecular Markers in Phyllostachys edulis

MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons lacking transposable enzyme sequences. It is abundant in eukaryotes genomes and is one of the most important driving forces for the formation of genomic polymorphism. In the present study, MITE Tracker, a novel software program, was used to identify MITEs in large genomes. A total of 1 579 MITEs families (18 373 full-length MITEs) in the latest genome version of Phyllostachys edulis (version 2018) were identified, accounting for 0.34% of the total genome of Ph. edulis. These MITEs families were clustered into seven super-families. The range of insertion time of the seven MITEs super-families was 0.5-16.5 mya. Three super-families might experience an expansion event during 2-4 mya. Two super-families might undergo two expansion events during 1-2 mya and 3-5 mya, respectively. Two super-families might experience a long expansion period during 0.5-16.5 mya. The MITEs in Ph. edulis genome preferred to insert into or near genes, and the Micron-like super-family preferred to insert between ATT and ATA regions. Furthermore, three pairs of primers were developed for the classification of the varieties and forms of Ph. violascens ‘Prevernalis’. In conclusion, the distribution, evolution and insertion of MITEs in P. edulis genome were analyzed and three molecular markers were obtained, which laid the foundation for further verification of MITEs function.

CSTR: 32200.14.cjcb.2021.02.0001