UC Riverside

Transposable elements (TE) are genetic elements, which can move within the genome. TE are widely distributed in almost all organisms, both prokaryotes and eukrayotes Nearly 45% of human genomes are constituted of transposable elements. There are two major classes of transposable elements: class I and class II. Class I elements, also called retrotransposons, use a so-called "copy and paste" mechanism to replicate them and insert into new positions via an RNA intermediate. Class II elements, also called DNA transposons, don't use an RNA intermediate but a "cut and paste" mechanism to move within genomes. In some filamentous fungi, there is a genome defense mechanism called Repeat-induced Point mutation (RIP) which causes C:G to T:A mutations to transposons regions and thus repress their transposition. My research involved characterization and annotation of transposable elements in seven filamentous fungi and RIP analysis in these species. I've developed an integrated pipeline for TE identification and annotation and found evidence of RIP using the RIP indices in 5 filamentous ascomycete fungi (Neurospora crassa, Neurospora tetrasperma, Neurospora discreta, Sporotrichum thermophile, and Thielavia terrestris), but no evidence of RIP in Chaetomium globosum and Sordaria macrosporus. I found that Gyspy and Copia LTRs were the most abundant TEs. My results presented two paradoxes: 1) S.macrospora and C.globosum have low percentage of interspersed repeats but lack evidence for RIP; 2) S.thermophile and T.terrestris show evidence for RIP but also have many repeats. Moreover, I've discovered several factors related to RIP mechanism, such as the length of transposons, the type of transposons, etc.