Miniature Inverted-repeat Transposable Elements (MITEs) Play Important Roles In Gene Expression And Species Diversity In Rice And Evolution Of Tomato Specific MiRNA Gene

Miniature inverted-repeat transposable elements (MITEs) are truncated autonomous DNA transposons. MITEs exhibit the structural features of DNA transposons, containing terminal inverted repeats (TIRs) flanked by small direct repeats (target site duplication, TSD). The internal sequences of MITEs are short and devoid of coding sequences of transposase. MITEs transpose through transposases encoded by autonomous DNA transposons. MITEs often have high copy numbers in genome. The diversity and evolutionary patterns may vary considerably in different MITE families. The genetic and evolutionary mechanisms of MITE amplification and accumulation in a species remain poorly understood. MITEs were shown to be mainly distributed on chromosome arms and highly associated with genes. The observed close physical association between MITEs and plant genes has provoked the hypothesis that MITEs play important roles in gene regulation and genome evolution. To better understand the role of MITEs on genome evolution, it is critical to systemically identify nearly all MITEs in genome and analyze the effects of MITE on gene expression and genome diversity. In this study, we developed a BLASTN-based approach for de novo identification of MITEs and systematically analyzed MITEs in rice genome. The genome of rice cultivar Nipponbare (Oryza sativa ssp. japonica) harbors178,533MITE-related sequences classified into6superfamilies and338families. These MITEs randomly distributed on noncoding regions of chromosome arms. Pairwise nucleotide diversity and phylogenetic tree analysis indicated that individual MITE families were resulted from one or multiple rounds of amplification bursts. The timing of amplification burst varied considerably between different MITE families or subfamilies. Approximately14.8%of loci with full-length MITEs have presence/absence polymorphism between rice cultivars93-11(O. sativa ssp. indica) and Nipponbare. MITEs are associated with23,623(58.2%) genes in rice genome. At least7,887MITEs are transcribed and more than3,463were transcribed with rice genes. The MITE sequences transcribed with rice coding genes form1,130pairs of potential natural sense/antisense transcripts. MITEs generate23.5%(183,837of781,885) of all small RNAs identified from rice. Some MITE families generated small RNAs mainly from the terminals, while other families generated small RNAs predominantly from the central region. More than half (51.8%) of the MITE-derived small RNAs were generated exclusively by MITEs located away from genes. Genome-wide analysis showed that genes associated with MITEs have significantly lower expression than genes away from MITEs. Considering the polymorphisms induced by MITE loci, MITEs provide considerable diversity for O. sativa.MicroRNA (miRNA) is a type of endogenous non-coding small RNA with length of20-24nt. It can regulate gene expression through inhibit translation or trigger degradation of target mRNA by base pairing with target mRNA. MIRNA gene structure and miRNA pathway vary between plants and animals. More and more miRNAs were identified by high-thoughput small RNA sequencing. Some miRNAs are conserved among most plant families, whileothers are species or linkage specifics, which are regarded as "young" miRNAs. There have been several models to explain how plant generated a short reverse complementary sequence and evolved to a new MIRNA gene. In this study, we identified213and266miRNAs in tomato and potato genomes according to public small RNA-seq data, respectively. Of them76and97were novel miRNA. Of the213MIRNA genes in tomato,70are not present in other genomes, and were considered as tomato specific MIRNA gene. Almost a half (45.7%) of tomato specific MIRNA genes are distributed in introns, and51.4%overlapped with transposable elements. This proportion is much higher than that of conserved tomato MIRNA genes. The flanking50kb sequence of75.7%(53) tomato specific MIRNA genes have syntenic region in potato genome, but only52.9%(37) of them can find allelic loci of MIRNA genes. We designed primers according to the flanking sequences of some loci and amplified PCR products in other Solanum species. Sequence analysis detected different evolutionary events, such as inverted duplication, short insertion or deletion, long insertion or deletion. It seems that the proportion of tomato novel MIRNA genarated from inverted duplications is not large, during the differentiation from Solanum ancester. A newly identified tomato specific MIRNA locus, sly-newt22, may have been derived from inter-chromosome transposition through flanking LTRs along the differentiation between tomato and potato. During the speciation of tomato, newt22locus lost serveral fragments and became a mature MIRNA gene which may regulate stress tolerance of tomato. Overall, our results provided novel insights on miRNA evolution, diversification and regulation in tomato.