Academic journal article Genetics

Chromosome Complement of the Fungal Plant Pathogen Fusarium Graminearum Based on Genetic and Physical Mapping and Cytological Observations

Academic journal article Genetics

Chromosome Complement of the Fungal Plant Pathogen Fusarium Graminearum Based on Genetic and Physical Mapping and Cytological Observations

Article excerpt

ABSTRACT

A genetic map of the filamentous fungus Fusarium graminearum (teleomorph: Gibberella zeae) was constructed to both validate and augment the draft whole-genome sequence assembly of strain PH-1. A mapping population was created from a cross between mutants of the sequenced strain (PH-1, NRRL 31084, originally isolated from Michigan) and a field strain from Minnesota (00-676, NRRL 34097). A total of 111 ascospore progeny were analyzed for segregation at 235 loci. Genetic markers consisted of sequence-tagged sites, primarily detected as dCAPS or CAPS (n = 131) and VNTRs (n = 31), in addition to AFLPs (n = 66) and 7 other markers. While most markers exhibited Mendelian inheritance, segregation distortion was observed for 25 predominantly clustered markers. A linkage map was generated using the Kosambi mapping function, using a LOD threshold value of 3.5. Nine linkage groups were detected, covering 1234 cM and anchoring 99.83% of the draft sequence assembly. The nine linkage groups and the 22 anchored scaffolds from the sequence assembly could be assembled into four chromosomes, leaving only five smaller scaffolds (59,630 bp total) of the nuclear DNA unanchored. A chromosome number of four was confirmed by cytological karyotyping. Further analysis of the genetic map data identified variation in recombination rate in different genomic regions that often spanned several hundred kilobases.

FUSARIUM graminearum Schwabe, a haploid ascoJ. rnycetous fungus and the major causal agent of Fusarium head blight (FHB) disease of small grain cereal crops, has received considerable attention by the scientific community due to severe disease outbreaks in the United States since 1992 (McMuLLEN et al. 1997). These epidemics resulted in heavy yield losses, which were exacerbated by the fact that FHB-infected grain is often contaminated with trichothecene mycotoxins and estrogenic compounds that pose a serious threat to food and feed safety. Largely because outbreaks of the disease occurred only sporadically throughout the last century, the fungus and the disease were poorly studied before the 1990s. Since then, considerable resources (for example, through the U.S. Wheat and Barley Scab Initiative, www.scabusa.org) have been allocated to study the biology, toxicology, and epidemiology of the pathogen and to explore potential control measures, especially through plant varietal development and biotechnology.

Due to this national and international interest [the pathogen also causes serious problems in Canada, Asia, Europe, and parts of South America (McMuLLEN et al. 1997)], F. graminearum was identified as a priority for whole-genome sequencing by the Broad Institute's Fungal Genome Initiative and in spring 2003 became the second plant-pathogenic fungus for which the wholegenome sequence has been made publicly available (http://www.broad.mit.edu). While a formal report detailing its genome structure is forthcoming, some generalizations can be made. Repetitive or even duplicated DNA is rare (GALE et al. 2002), and a preliminary report indicated that its karyotype consists of only four chromosomes (M. TAGA, C. WAALWIJK, W. G. FLIER and G. H. J. KEMA, unpublished results), a very low number compared to that in other filamentous fungi (e.g., ZOLAN 1995). Perhaps due to these characteristics, the draft genome assembly of F. graminearum is remarkably complete, having fewer and larger scaffolds (supercontigs) than the assemblies of four other filamentous ascomycetous fungi (Magnaporthegrisea, Neurospora crassa, Aspergillus nidulans, and Staganospora nodorum) of comparable genome size (30-40 Mb) and sequencing coverage (7- to 13-fold). Despite the high quality of the F. graminearum draft sequence assembly, physical alignment of scaffolds into chromosomes has not been possible. The pulsed-field gel electrophoresis method that allows for separation and quantification of chromosomes for many fungi is not useful for F. graminearum because its chromosomes are comparatively large and similar in size. …

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