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.
Genomics, Fungi, Clusters, Gene Position
Level of Degree
UNM Biology Department
First Committee Member (Chair)
Second Committee Member
Third Committee Member
Martinez, Antonio Diego. "Genome architecture in the fungal kingdom." (2010). https://digitalrepository.unm.edu/biol_etds/76