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Title:   Author  item
                                            DHILLON, BRAHAM - University Of British Columbiaitem
                                            GILL, NAVDEEP - University Of British Columbiaitem
                                            HAMELIN, RICHARD - University Of British Columbiaitem
                                            Goodwin, Stephen

                                                         - *Steve*
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 12/12/2014
                                    Publication  Date: 12/17/2014
                                    Citation: Dhillon, B., Gill, N., Hamelin, R., Goodwin, S.B. 2014. The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola. Biomed Central (BMC) Genomics. 15:1132.Interpretive Summary: The genome of the wheat pathogen Mycosphaerella graminicola has been sequenced completely, but its repetitive fraction has been characterized only poorly. Repetitive sequence analysis has become an integral part of genome sequencing projects to improve gene prediction, but also because of the role that repetitive sequences play in determining the structure and evolution of genes and genomes. To improve annotation of the M. graminicola genome, four independent approaches were used to identify and characterize the repetitive fraction. Approximately 17% of the M. graminicola genome was estimated to be repetitive, mostly due to retrotransposons, which amplify by a copy-and-paste mechanism and account for ~70% of the total repetitive content. Non-essential chromosomes had a higher percentage of repetitive elements compared to the core set. Six chromosomes showed a non-random distribution of repetitive elements with much clustering. All repeat families contained changes consistent with repeat-induced point mutation, a process for inactivating transposons in fungi. All chromosomes had repetitive elements at their ends, including two families of repetitive elements that were only found at chromosome ends. The variable distribution of repetitive content across chromosomes suggests possible evolutionary constraints. The thorough and highly curated database of repetitive sequences that was generated through this project will be very useful to bioinformaticists looking to characterize the repetitive fractions of the genomes of other organisms, to evolutionary biologists working to understand the effect of repetitive elements on gene and genome evolution, and to plant pathologists trying to manage the wheat disease caused by this organism.
                                Technical Abstract: Repetitive sequence analysis has become an integral part of genome sequencing projects in addition to gene identification and annotation. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining the structure and evolution of genes and genomes. Four independent approaches were used to identify and characterize the repetitive fraction of the finished genome of the wheat pathogen Mycosphaerella graminicola. This ascomycete fungus has a genome of 21 chromosomes, eight of which are dispensable. Approximately 17% of the M. graminicola genome was estimated to be repetitive. Class I transposable elements account for ~70% of the total repetitive content in the M. graminicola genome. The dispensable chromosomes had a higher percentage of repetitive elements compared to the core chromosomes. The distribution of repeats across chromosomes also varied, with at least six chromosomes showing a non-random distribution. Repeat families showed transition mutations and a CpA to TpA dinucleotide bias, indicating a repeat-induced point mutation-like mechanism in M. graminicola. A total of 78 putative clusters of nested elements was found in the M. graminicola genome. Length of subtelomeric regions varied with chromosome; two repeat families and one gene family specific to subtelomeres were identified. Apart from characterizing the transposable elements, a thorough and highly curated database of repetitive sequences also was generated. Results show that the repetitive content and distribution (random vs. clustered) varies across chromosomes, suggesting that different chromosomes could be subject to different evolutionary constraints.


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