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Genome architecture in the fungal kingdom

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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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Title: Genome architecture in the fungal kingdom
Author: Martinez, Antonio Diego, 1971-
Advisor(s): Nelson, Mary Anne
Committee Member(s): Werner-Washburne, Margaret
Lane, Terran
Baker, Scott
Department: University of New Mexico. Biology Dept.
Subject: Genomics
Fungi
Clusters
Gene Position
LC Subject(s): Genomes
Genomics
Fungi--Genetics
Degree Level: Doctoral
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.
Graduation Date: July 2010
URI: http://hdl.handle.net/1928/10887


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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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