MITE类转座子mPing在水稻不同亚种间的差异分析

Comparison of MITE transposons mPing in different rice subspecies

mPing是水稻中第一个被鉴定出的有活性的MITE类转座子,为了探索mPing在水稻粳稻品种日本晴和籼稻品种93-11基因组中的分布差异,本研究首先运用Southern杂交的方法初步检测m Ping在两个亚种中拷贝数的差异,然后通过同源性探寻方法发现,m Ping在水稻亚种日本晴和93-11基因组中拷贝数分别为52和14,并且日本晴基因组中的m Ping均为m Ping-1,93-11中m Ping-1的拷贝数为3,m Ping-2的拷贝数为11。通过分析m Ping上下游5 kb侧翼序列发现m Ping在日本晴和93-11中分别与23和3个已知基因相关联。本研究为阐明以m Ping的分布多样性为主要原因的粳稻和籼稻之间的遗传差异提供初步理论基础。

The m Ping family is the first active MITE TE family identified in rice genome. In order to compare the compositions and distributions of m Ping family in the genomes of two rice subspecies japonica（cv. Nipponbare） and indica（cv. 93-11）, we initially estimated the copy numbers of m Ping 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 m Ping copies in corresponding reference genome, respectively. All m Ping members in Nipponbare genome belong to m Ping-1, while there are 3 m Ping-1 and 11 m Ping-2 copies in 93-11 genome. By further investigating the 5-kb flanking sequences of those m Ping copies, it was found that 23 and 3 protein-coding genes in Nipponbare and 93-11 genome are residing adjacent to those m Ping 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 m Ping.