Gene loss in the fungal canola pathogen Leptosphaeria maculans
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Recent comparisons of the increasing number of genome sequences have revealed that variation in gene content is considerably more prevalent than previously thought. This variation is likely to have a pronounced effect on phenotypic diversity and represents a crucial target for the assessment of genomic diversity. Leptosphaeria maculans, a causative agent of phoma stem canker, is the most devastating fungal pathogen of Brassica napus (oilseed rape/canola). A number of L. maculans genes are known to be present in some isolates but lost in the others. We analyse gene content variation within three L. maculans isolates using a hybrid mapping and genome assembly approach and identify genes which are present in one of the isolates but missing in the others. In total, 57 genes are shown to be missing in at least one isolate. The genes encode proteins involved in a range of processes including oxidative processes, DNA maintenance, cell signalling and sexual reproduction. The results demonstrate the effectiveness of the method and provide new insight into genomic diversity in L. maculans.
KeywordsNGS Re-sequencing Gene loss Gene content variation Leptosphaeria maculans
The authors would like to acknowledge the funding support from the Australian Research Council (Projects LP0882095, LP0883462, LP0989200, LP110100200 and DP0985953).
- Fitt BD, Evans N, Howlett BJ, Cooke M (2006) Sustainable strategies for managing Brassica napus (oilseed rape) resistance to Leptosphaeria maculans (phoma stem canker) vol 114. SpringerGoogle Scholar
- Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997–1002Google Scholar
- Raffaele S, Kamoun S (2012) Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Micro 10:417–430Google Scholar
- Syme RA, Hane JK, Friesen TL, Oliver RP (2013) Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. G3: Genes|Genomes|Genetics 3:959–969Google Scholar
- URGI Unite Recherche Genomique Info (2010) Plant and fungi data integration. URGI. http://urgi.versailles.inra.fr/Species/Leptosphaeria/Sequences-Databases/Download. 2014
- Van de Wouw AP, Cozijnsen AJ, Hane JK, Brunner PC, McDonald BA, Oliver RP, Howlett BJ (2010) Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathog 6:e1001180. doi: 10.1371/journal.ppat.1001180 CrossRefPubMedCentralPubMedGoogle Scholar
- Wickham H (2009) ggplot2: elegant graphics for data analysis. New YorkGoogle Scholar