Making sense of repetitive sequences in the genus Mycosphaerella
Abstract
Repetitive sequences are an integral part of all the genomes studied so far. Previously labeled as ‘junk’, numerous studies have implicated repetitive sequences in important biological and structural roles in the genome. With this in mind, the repetitive fraction for two fungal genomes in the genus Mycosphaerella was analyzed. Repeats were identified de novo using several methods. All repeat families carried a very high number of transition mutations, characteristic of Repeat-Induced Point mutations (RIP). In M. graminicola, many repeats were inserted into other repeats forming nested clusters. Analyses of M. graminicola repeat sequences uncovered a repetitive family carrying a DNA methyltransferase (DNMT) sequence. A single-copy gene in eleven other fungal species analyzed, it had expanded to 22 copies in M. graminicola. Southern analysis confirmed multiple DNMT copies across a diverse array of 15 M. graminicola isolates. Amplification was countered by RIP inactivation of all DNMT copies and completely eliminating cytosine methylation, as determined by ESI-MS/MS. Presence of methylation in S1, a Mycosphaerella species from wild grass, that diverged from M. graminicola 10,500 years ago, indicates loss of methylation to be a recent event, concomitant with the domestication of wheat as a crop. We speculate that the loss of methylation may have facilitated the switch of M. graminicola from a wild host to domesticated wheat and assisted its evolution as a plant pathogen. Repetitive sequence analysis of M. fijiensis, a close relative of M. graminicola , revealed a similar but independent amplification of an essential gene, histone H3. Characterization of M. fijiensis repeats also demonstrated that an amplification of LTR retrotransposons was the primary cause of genome expansion in M. fijiensis. These findings support the existing hypothesis that, in addition to being one of the primary drivers of genome structure evolution, repetitive elements can profoundly influence the evolution and biology of an organism.
Degree
Ph.D.
Advisors
Goodwin, Purdue University.
Subject Area
Bioinformatics
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