Habitat-Defining Genes and Synteny of Conditionally Dispensable (CD) Chromosomes in the Fungus Nectria Haematococca

Persistent Link:
http://hdl.handle.net/10150/194482
Title:
Habitat-Defining Genes and Synteny of Conditionally Dispensable (CD) Chromosomes in the Fungus Nectria Haematococca
Author:
Rodriguez, Marianela
Issue Date:
2006
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Individual isolates of the fungus Nectria haematococca exist in a wide range of habitats and part of this diversity is attributed to the presence of conditionally dispensable (CD) chromosomes that carry habitat-defining genes. In the current study a new factor located on one of these CD chromosomes was found. This trait allows pea pathogenic isolates of N. haematococca to grow in homoserine, a compound present in large amounts on pea root exudates. The gene(s) for homoserine utilization (HUT) are located on the same CD chromosome that carries the cluster of genes for pea pathogenicity, the PEP cluster. The PDA1 gene, a member of the PEP cluster, is routinely used as a marker for the presence of this CD chromosome, therefore it has been called the PDA1-CD chromosome. For the purpose of identifying the HUT gene(s), a physical map of the PDA1-CD chromosome was constructed. This map, in combination with synteny analysis, and Southern hybridizations led to the identification of a region of 365Kb that is likely to contain the HUT gene. By searching the publicly available genome of N. haematococca several candidates for HUT were identified.The synteny evaluation between the PDA1-CD chromosome and a different CD chromosome that carries the MAK1 gene, for chickpea pathogenicity, revealed a region (> 463Kb) of synteny, which advocates for a common ancestor for these CD chromosomes. However a large region (~ 1 Mb) in each of the CD chromosomes was found to carry unique DNA, therefore we proposed that individual isolates of this fungus contain large regions of unique DNA located on the CD chromosomes. The localization of syntenic regions also suggests that breakage points previous identified in the MAK1-CD chromosome could potentially be "hot spots" for recombination between both CD chromosomes. Furthermore, the anchoring of the PDA1-CD map to the genome of N. haematococca allowed the identification of additional putative habitat colonization genes present on both CD chromosomes, and niche-defining genes on the PDA1-CD chromosome.
Type:
text; Electronic Dissertation
Keywords:
CD chromosomes; Nectria haematococca; Homoserine; Fusarium; rhizosphere
Degree Name:
PhD
Degree Level:
doctoral
Degree Program:
Plant Pathology; Graduate College
Degree Grantor:
University of Arizona
Advisor:
VanEtten, Hans D.
Committee Chair:
VanEtten, Hans D.

Full metadata record

DC FieldValue Language
dc.language.isoENen_US
dc.titleHabitat-Defining Genes and Synteny of Conditionally Dispensable (CD) Chromosomes in the Fungus Nectria Haematococcaen_US
dc.creatorRodriguez, Marianelaen_US
dc.contributor.authorRodriguez, Marianelaen_US
dc.date.issued2006en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractIndividual isolates of the fungus Nectria haematococca exist in a wide range of habitats and part of this diversity is attributed to the presence of conditionally dispensable (CD) chromosomes that carry habitat-defining genes. In the current study a new factor located on one of these CD chromosomes was found. This trait allows pea pathogenic isolates of N. haematococca to grow in homoserine, a compound present in large amounts on pea root exudates. The gene(s) for homoserine utilization (HUT) are located on the same CD chromosome that carries the cluster of genes for pea pathogenicity, the PEP cluster. The PDA1 gene, a member of the PEP cluster, is routinely used as a marker for the presence of this CD chromosome, therefore it has been called the PDA1-CD chromosome. For the purpose of identifying the HUT gene(s), a physical map of the PDA1-CD chromosome was constructed. This map, in combination with synteny analysis, and Southern hybridizations led to the identification of a region of 365Kb that is likely to contain the HUT gene. By searching the publicly available genome of N. haematococca several candidates for HUT were identified.The synteny evaluation between the PDA1-CD chromosome and a different CD chromosome that carries the MAK1 gene, for chickpea pathogenicity, revealed a region (> 463Kb) of synteny, which advocates for a common ancestor for these CD chromosomes. However a large region (~ 1 Mb) in each of the CD chromosomes was found to carry unique DNA, therefore we proposed that individual isolates of this fungus contain large regions of unique DNA located on the CD chromosomes. The localization of syntenic regions also suggests that breakage points previous identified in the MAK1-CD chromosome could potentially be "hot spots" for recombination between both CD chromosomes. Furthermore, the anchoring of the PDA1-CD map to the genome of N. haematococca allowed the identification of additional putative habitat colonization genes present on both CD chromosomes, and niche-defining genes on the PDA1-CD chromosome.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectCD chromosomesen_US
dc.subjectNectria haematococcaen_US
dc.subjectHomoserineen_US
dc.subjectFusariumen_US
dc.subjectrhizosphereen_US
thesis.degree.namePhDen_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplinePlant Pathologyen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorVanEtten, Hans D.en_US
dc.contributor.chairVanEtten, Hans D.en_US
dc.contributor.committeememberVanEtten, Hans D.en_US
dc.contributor.committeememberHawes, Martha C.en_US
dc.contributor.committeememberOrbach, Marc J.en_US
dc.contributor.committeememberDieckmann, Carol L.en_US
dc.contributor.committeememberGoll, Darrel E.en_US
dc.identifier.proquest1754en_US
dc.identifier.oclc659747515en_US
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