Honors College Thesis
 

De novo Discovery of Novel Long Noncoding RNAs in the North American Beaver

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https://ir.library.oregonstate.edu/concern/honors_college_theses/vh53x179v

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  • Long noncoding RNAs (lncRNAs) are RNA molecules that are at least 200 nucleotides long and do not encode proteins. lncRNAs have roles in gene regulation, chromatin epigenetics, and molecular scaffolding. In light of mounting evidence implicating species-specific noncoding RNAs and gene regulatory mechanisms in species adaptations, it is reasonable to speculate that species-specific lncRNAs may underlie some of the adaptations seen in mammalian evolution. The genome and transcriptome of the North American beaver (Castor canadensis, a keystone species of northwest wetlands) have recently been sequenced for the first time, enabling a search for genomic adaptations of this unique semi-aquatic herbivore. The objective of this study was to identify novel lncRNAs in the beaver using a computational analysis of high throughput sequencing data from Oregon State University’s recently-released beaver genome and a pan-tissue composite transcriptome that we obtained from 16 tissues from a beaver. We found 182 novel lncRNAs and 113 lncRNAs with a known ortholog in another species. Nine candidate lncRNAs stood out for having the strongest evidence across the various performance measures. One novel lncRNA (contig62060.1) was the only putative novel multi-exonic lncRNA we detected. These novel lncRNAs may serve as a basis for hypothesis generation for targeted functional investigations.
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  • This work was funded in part by OSU College of Veterinary Medicine Biomedical Sciences Student Summer Research Program (Summer 2016).
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  • Pending Publication
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  • 2018-01-03 to 2018-08-02

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