Degree Type

Dissertation

Date of Award

2008

Degree Name

Doctor of Philosophy

Department

Theses & dissertations (Interdisciplinary)

Major

Bioinformatics and Computational Biology

First Advisor

Roger Wise

Second Advisor

Volker Brendel

Third Advisor

Xun Gu

Abstract

Sequencing projects continue to tackle larger and more challenging genomes. Many of the grass genomes have important agriculture and economic impacts. The maize genome is now underway, and others important as foods and biofuels will be sequenced in the near future. The grass genomes are very large and therefore computationally complex to assemble and annotate. Long terminal repeat retrotransposons make up significant portions of many of the longer grass genomes. Their repeat sequences across the genome, their terminal repeats, and their nested cluster configuration make assembly of sequence clones challenging and identification of gene regions difficult. Tools are needed to assist with the more difficult types of genomes that are sequenced today and will be sequenced in the future. Sequencing of the maize genome is underway, but still much is not known about the landscape of the genome. While many smaller regions of maize have been sequenced, they cannot give a full picture of the structure and layout of gene islands and of repeat clusters. In addition, because of the available small sequenced contigs of maize, a true view of the relationships between maize and other grass genomes remains elusive. In this thesis I provide tools necessary for both assembly and annotation of highly repetitive genomes, and I use these tools to construct the currently two longest maize sequence contigs. These contigs provide a resource for many of the unanswered questions of the maize genome.

DOI

https://doi.org/10.31274/rtd-180813-16960

Publisher

Digital Repository @ Iowa State University, http://lib.dr.iastate.edu/

Copyright Owner

Brent Anson Kronmiller

Language

en

Proquest ID

AAI3330843

OCLC Number

294847592

ISBN

9780549871774

File Format

application/pdf

File Size

116 pages

Share

COinS