Electronic Theses and Dissertations

Identifier

637

Date

2012

Document Type

Thesis

Degree Name

Master of Science

Major

Bioinformatics

Committee Member

Duane D. McKenna

Committee Member

Ramin Homayouni

Committee Member

Thomas R. Sutter

Abstract

Our knowledge of beetle cytochrome P450 (CYP) genes was primarily obtained from studies of the model beetle and grain pest Tribolium castaneum.To gain additional insight into beetle CYPs and ultimately to inform our understanding of beetle CYP evolution, we identified and annotated all of the CYP genes present in a new draft genome of Harmonia axyridis by using traditional and automated methods for gene annotation. Overall, we identified somewhat fewer CYPs in H. axyridis (at least 94 genes and 3 pseudo genes representing 17 families and 42 subfamilies) compared to the number of of known CYPs in T. castaneum (137 plus 2 slight variants and 10 pseudogenes). The H. axyridis CYPs could be divided into 4 distinct clans: Mito, CYP2, CYP3 and CYP4 clans are major (monophyletic ) groups with strong support for most relationships and illustrates the presence of CYP "blooms" in T. castaneum that are lacking in H. axyridis. Several additional CYPs that are present in H. axyridis are missing in T. castaneum. The Mito clan of H. axyridis contains 6 genes in 5 families and 6 subfamilies . We found 7 genes in CYP2 clan with 5 families and 6 sub-families. We found 2 distinct families (4 and 349) and a minimum of 22 genes in the CYP4 clan in H. axyridis. Interestingly, both H. axyridis and T. castaneum carry CYP4G genes, which are candidate resistance genes for insecticides, including permethrins. The function of CYP4G was associated with pesticide resistance. The CYP3 clan has 59 genes in t families in 5 families H.axyridis: CYP6, CYP9, CYP345, CYP435 and CYP436. These 5 families in CYP3 are classified into at least 21 subfamilies. Our work focused on the automated annotation of CYP genes involved several software programs, the most efficient and sensitive of which are Augustus, GenScan and Fgenesh. Although it is likely that a few CYP genes remain to be identified in H.axyridis genome, our ongoing work suggests that the vast majority of CYPs have been identified.

Comments

Data is provided by the student.

Library Comment

Dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.

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