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Genome architecture in the fungal kingdom


Please use this identifier to cite or link to this item: http://hdl.handle.net/1928/10887

Genome architecture in the fungal kingdom

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dc.contributor.author Martinez, Antonio Diego, 1971-
dc.date.accessioned 2010-06-28T21:55:11Z
dc.date.available 2010-06-28T21:55:11Z
dc.date.issued 2010-06-28T21:55:11Z
dc.date.submitted July 2010
dc.identifier.uri http://hdl.handle.net/1928/10887
dc.description.abstract Previous studies have suggested that the location of genes in genomes is not random; instead they may be organized in a way that is beneficial to cellular processes and the organism. While a few studies have investigated the organization of genes on a whole genome scale, they were limited in the functions of genes used in the search and in the number and type of genomes searched. With the recent explosion of available fungal genomes and tools to automatically annotate many genes in a short period of time, it is now possible to obtain a global view of the level of clustering in the genomes of an entire kingdom. To find gene clusters in many genomes, we have constructed a robust and flexible algorithm that runs in trivial time. In parallel, we have annotated 72 fungal genomes using four automated annotation tools that provide information about protein function, protein targeting, involvement in biochemical pathways and paralogous gene families. We used the clustering algorithm to search for clusters from the four annotation categories. We discovered that all the genomes contained clusters of related genes, and that in several cases the clusters included genes involved in processes that were specific to the species in which they are found. This has dramatically expanded our knowledge of both the types of clusters and the number of genomes known to contain clusters. This study has generated information that will assist researchers in addressing many questions central to molecular and cell biology as well as evolutionary studies. en_US
dc.language.iso en_US en_US
dc.subject Genomics en_US
dc.subject Fungi en_US
dc.subject Clusters en_US
dc.subject Gene Position en_US
dc.subject.lcsh Genomes
dc.subject.lcsh Genomics
dc.subject.lcsh Fungi--Genetics
dc.title Genome architecture in the fungal kingdom en_US
dc.type Dissertation en_US
dc.description.degree Biology en_US
dc.description.level Doctoral en_US
dc.description.department University of New Mexico. Biology Dept. en_US
dc.description.advisor Nelson, Mary Anne
dc.description.committee-member Werner-Washburne, Margaret
dc.description.committee-member Lane, Terran
dc.description.committee-member Baker, Scott

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Files Size Format View Description
Diego 5-4-10 Final.pdf 3.499Mb PDF View/Open Main Dissertation
SupplementaryTable1_txt.gz 684.2Kb Text file View/Open Supplementary Statistical Measures of Clusters
SupplementaryTable2_txt.gz 10.89Kb Text file View/Open All Clusters

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