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Genetic Linkage Maps and Genomic Organization in Leptosphaeria maculans

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Abstract

Leptosphaeria maculans is a haploid outcrossing ascomycete with a genome size of about 34 Megabases (Mb) which is predicted to have between 10,000 and 12,000 genes. The chromosomes of L. maculans are of a size range (0.7–3.5 Mb) and number (15–16) that can be readily resolved by pulsed field gel electrophoresis. Chromosome length polymorphisms are generated by meiosis giving rise to size differences as high as 57%, in the case of the ribosomal DNA-harbouring chromosome whose size varies between 1.8 and 4.2 Mb. Genetic maps are characterised by linkage groups comprising an accumulation of markers based on retrotransposon sequences. This, along with sequencing of pericentromeric regions and stretches of ORF-rich regions, suggest that the genome of L. maculans consists of a mosaic of GC-equilibrated coding regions with no or few transposons, and of stretches of highly degenerated and truncated retrotransposons, encompassing very few genes. Chromosome length polymorphisms are linked with the loss of dispensable regions. We suggest that the degree of length polymorphism for a particular chromosome correlates to the amount of dispensable retrotransposons, and that some gene-rich chromosomes may be less prone to undergo chromosome length polymorphisms than other chromosomes.

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Abbreviations

AFLP:

amplified fragment length polymorphism

BAC:

bacterial artificial chromosome

CHEF:

contour-clamped homogeneous electric field

CLP:

chromosome length polymorphism

ISSR:

inter-simple sequence repeat

LG:

linkage group

LTR:

long terminal repeats

RAPD:

random amplified polymorphic DNA

Rep-PCR:

repetitive element-based PCR

RIP:

repeat induced point mutation

TAFE:

transverse alternating field electrophoresis

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Author notes

  1. Delphine Melayah

    Present address: Laboratoire d’Ecologie Microbienne, Université Claude Bernard Lyon 1, 69622, Villeurbane cedex, France

Authors and Affiliations

  1. INRA-PMDV, Route de St Cyr, 78026 , Versailles Cedex, France

    Marie-Line Kuhn, Lilian Gout, Delphine Melayah, Michel Meyer, Marie-Hélène Balesdent & Thierry Rouxel

  2. Protection des Plantes, INA-PG, F-78850, Thiverval-Grignon, France

    Lilian Gout

  3. School of Botany, The University of Melbourne, 3010, Victoria, Australia

    Barbara J. Howlett

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  1. Marie-Line Kuhn
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  2. Lilian Gout
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Correspondence to Thierry Rouxel.

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Kuhn, ML., Gout, L., Howlett, B.J. et al. Genetic Linkage Maps and Genomic Organization in Leptosphaeria maculans . Eur J Plant Pathol 114, 17–31 (2006). https://doi.org/10.1007/s10658-005-3168-6

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