title: The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola.
abstract: BACKGROUND
  In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. 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. Several methods using different repeat-finding strategies are available for whole-genome repeat sequence analysis. Four independent approaches were used to identify and characterize the repetitive fraction of the Mycosphaerella graminicola (synonym Zymoseptoria tritici) genome. This ascomycete fungus is a wheat pathogen and its finished genome comprises 21 chromosomes, eight of which can be lost with no obvious effects on fitness so are dispensable.
  
  
  RESULTS
  Using a combination of four repeat-finding methods, at least 17% of the M. graminicola genome was estimated to be repetitive. Class I transposable elements, that amplify via an RNA intermediate, account for about 70% of the total repetitive content in the M. graminicola genome. The dispensable chromosomes had a higher percentage of repetitive elements as compared to the core chromosomes. Distribution of repeats across the chromosomes also varied, with at least six chromosomes showing a non-random distribution of repetitive elements. Repeat families showed transition mutations and a CpA → TpA dinucleotide bias, indicating the presence of a repeat-induced point mutation (RIP)-like mechanism in M. graminicola. One gene family and two repeat families specific to subtelomeres also were identified in the M. graminicola genome. A total of 78 putative clusters of nested elements was found in the M. graminicola genome. Several genes with putative roles in pathogenicity were found associated with these nested repeat clusters. This analysis of the transposable element content in the finished M. graminicola genome resulted in a thorough and highly curated database of repetitive sequences.
  
  
  CONCLUSIONS
  This comprehensive analysis will serve as a scaffold to address additional biological questions regarding the origin and fate of transposable elements in fungi. Future analyses of the distribution of repetitive sequences in M. graminicola also will be able to provide insights into the association of repeats with genes and their potential role in gene and genome evolution.
authors.affiliation: Department of Forest and Conservation Sciences, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. dhillonb@mail.ubc.ca.
authors.forename: Braham
authors.initials: B
authors.lastname: Dhillon
authors.affiliation: Department of Botany, Beaty Biodiversity Centre, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada. navdeep.gill@botany.ubc.ca.
authors.forename: Navdeep
authors.initials: N
authors.lastname: Gill
authors.affiliation: Department of Forest and Conservation Sciences, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. richard.hamelin@ubc.ca.|Natural Resources Canada, Laurentian Forestry Centre, 1055 du PEPS, Stn. Sainte-Foy, P.O. Box 10380, Quebec, QC, G1V 4C7, Canada. richard.hamelin@ubc.ca.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Hamelin
authors.affiliation: USDA-ARS, Crop Production and Pest Control Research Unit, Purdue University, 915 W. State Street, West Lafayette, Indiana, 47907-2054, USA. sgoodwin@purdue.edu.
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Goodwin
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000502:physiology*; D015825:Chromosomes, Fungal / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017354:Point Mutation; D020080:Tandem Repeat Sequences / Q000235:genetics; D016615:Telomere / Q000235:genetics; D014908:Triticum / Q000382:microbiology*
chemical_list: D004251:DNA Transposable Elements