Degree Type
Creative Component
Semester of Graduation
Fall 2018
Department
Computer Science
First Major Professor
Eve Wurtele
Second Major Professor
David Fernández-Baca
Degree(s)
Master of Science (MS)
Major(s)
Computer Science
Abstract
Orphan genes are the genes that lack detectable homologs in other species. Orphan genes also known as TRS (Taxonomically Restricted Genes) are an elliptical component of the genome because their ancestry and functions are mostly unknown. Understanding the functional significance and the origin of such orphan genes may give us insights into novel traits that can be evolutionary and physiologically important. Using bioinformatics computation and statistical analysis of Oryza sativa japonica, the total of 1,507 orphan genes was found. Around 5,173,767 unannotated open reading frames (ORFs) in Oryza sativa japonica genome which could be potential coding for a novel protein specific to Oryza sativa japonica is obtained. The publicly available RNAseq data from SRAdb were then used in order to explore the expression patterns of these orphan genes under various conditions. Most of the research disregards orphan genes as its importance and functions are not well known. Orphan genes are related to stress responses and specific traits which might be the key to improve crop yields and disease resistance in domestic plants.
Copyright Owner
Rakesh Shah
Copyright Year
2018
File Format
application/pdf
Recommended Citation
Shah, Rakesh, "Identification and characterization of orphan genes in rice (Oryza sativa japonica) to understand novel traits driving evolutionary adaptation and crop improvement." (2018). Creative Components. 103.
https://lib.dr.iastate.edu/creativecomponents/103
