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. To this end, the thousands of clusters we have discovered are available for download at kiddomics.com/.
Some files may require a special program or browser plug-in. More Information
|Advisor:||Nelson, Mary Anne|
|Commitee:||Baker, Scott, Lane, Terran, Werner-Washburne, Margaret|
|School:||The University of New Mexico|
|School Location:||United States -- New Mexico|
|Source:||DAI-B 71/07, Dissertation Abstracts International|
|Keywords:||Biofuels, Clustering, Fungi, Genomics|
Copyright in each Dissertation and Thesis is retained by the author. All Rights Reserved
The supplemental file or files you are about to download were provided to ProQuest by the author as part of a
dissertation or thesis. The supplemental files are provided "AS IS" without warranty. ProQuest is not responsible for the
content, format or impact on the supplemental file(s) on our system. in some cases, the file type may be unknown or
may be a .exe file. We recommend caution as you open such files.
Copyright of the original materials contained in the supplemental file is retained by the author and your access to the
supplemental files is subject to the ProQuest Terms and Conditions of use.
Depending on the size of the file(s) you are downloading, the system may take some time to download them. Please be