Comparison of MITE transposons mPing in different rice subspecies

Abstract:

The mPing family is the first active MITE TE family identified in rice genome. In order to compare the compositions and distributions of mPing family in the genomes of two rice subspecies japonica (cv. Nipponbare) and indica (cv. 93-11), we initially estimated the copy numbers of mPing family in those two subspecies using Southern blot and then confirmed the results by searching homologous copies in each reference genome using Blastn program, which turned out to have 52 and 14 mPing copies in corresponding reference genome, respectively. All mPing members in Nipponbare genome belong to mPing-1, while there are 3 mPing-1 and 11 mPing-2 copies in 93-11 genome. By further investigating the 5-kb flanking sequences of those mPing copies, it was found that 23 and 3 protein-coding genes in Nipponbare and 93-11 genome are residing adjacent to those mPing copies respectively. These results establish the preliminary theoretical foundation for further dissecting the genetic differences of japonica and indica rice in terms of the diversities and distributions of their component mPing.