The goal of this dissertation is to identify and analyze two of the noncoding genetic elements, microRNAs (miRNAs) and intorns, in plant genomes.

miRNAs are a class of short noncoding RNAs of which some are shown to regulate gene expression at the post-transcriptional level by complementary base pairing to their target mRNAs. In the early 2000s, a large number of miRNAs were cloned in animals, plants and viruses. Complementary efforts also sought to identify miRNA genes computationally. In the dissertation, I developed a computational method to identify miRNA genes and their target mRNAs in Arabidopsis. Experiments were then performed to validate some of the new miRNA genes and the miRNA-target interaction. The study facilitates the identification and characterization of conserved and non-conserved miRNAs in plants.

Another noncoding element discussed in the dissertation is intron. The removal of introns from precursor mRNAs (pre-mRNAs), which is called pre-mRNA splicing, is essential to produce mature mRNAs and proteins. Alternative splicing (AS) occurs when different patterns of splicing result from the same pre-mRNA. AS is important in regulated gene expression and has various effects on mRNAs and proteins. In the dissertation, I am interested in studying the role of splice site sequences in intron evolution and AS. In one chapter, software is developed to identify conserved intron positions within orthologous genes. I demonstrated its application to a set of plant-specific orthologous genes. In another chapter, I have developed a computational approach to identify transcript-confirmed introns and genes in 15 plant species and analyzed intron evolution in the context of orthology. The results indicate dynamic evolution of introns with different splice sites and the significance of splice site sequences during intron evolution. In a third chapter, by using the transcript-confirmed data, I identified AS introns and events in the 15 plant species and studied their behavior and effect on protein sequences. The findings underscore the important role of splice site sequences in AS regulation. In conclusion, the identification of transcript-confirmed introns and the study of intron evolution and AS provide insight into the significant role of splice site sequences in intron evolution and AS.