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Functional & Integrative Genomics

, Volume 15, Issue 2, pp 189–196 | Cite as

Gene loss in the fungal canola pathogen Leptosphaeria maculans

  • Agnieszka A. Golicz
  • Paula A. Martinez
  • Manuel Zander
  • Dhwani A. Patel
  • Angela P. Van De Wouw
  • Paul Visendi
  • Timothy L. Fitzgerald
  • David Edwards
  • Jacqueline BatleyEmail author
Original Paper

Abstract

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.

Keywords

NGS Re-sequencing Gene loss Gene content variation Leptosphaeria maculans 

Notes

Acknowledgments

The authors would like to acknowledge the funding support from the Australian Research Council (Projects LP0882095, LP0883462, LP0989200, LP110100200 and DP0985953).

Supplementary material

10142_2014_412_MOESM1_ESM.pdf (384 kb)
ESM 1 (PDF 383 kb)
10142_2014_412_MOESM2_ESM.pdf (188 kb)
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10142_2014_412_MOESM3_ESM.docx (19 kb)
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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Agnieszka A. Golicz
    • 1
    • 2
  • Paula A. Martinez
    • 1
    • 2
  • Manuel Zander
    • 1
    • 2
  • Dhwani A. Patel
    • 1
    • 2
  • Angela P. Van De Wouw
    • 3
  • Paul Visendi
    • 1
    • 2
  • Timothy L. Fitzgerald
    • 4
  • David Edwards
    • 1
    • 2
    • 5
  • Jacqueline Batley
    • 1
    • 5
    Email author
  1. 1.School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  2. 2.Australian Centre for Plant Functional Genomics and School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  3. 3.School of BotanyUniversity of MelbourneMelbourneAustralia
  4. 4.CSIRO Plant IndustryBrisbaneAustralia
  5. 5.School of Plant BiologyUniversity of Western AustraliaPerthAustralia

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