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A snapshot of the Artemia genome
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Text
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Title
A snapshot of the Artemia genome
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to code or not to code
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ETD_2189
Identifier
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http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000051922
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eng
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theses
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Topic
Microbiology and Molecular Genetics
Subject
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(authority = ETD-LCSH)
Topic
Artemia--Genetics
Subject
(ID = SBJ-3);
(authority = ETD-LCSH)
Topic
Genomes
Abstract
The Waksman Student Scholars Program, along with the Introduction to Molecular Biology and Biochemical Research class, were responsible for the publication of 628 Artemia sequences. Surprisingly, 361 of these sequences (58%) did not contain an open reading frame larger than 80 residues. It was originally presumed that this was due to a high level of genomic DNA contamination. While it is possible that some of our Artemia sequences are genomic contamination, I believe a large majority of our non-coding sequences are long non-coding RNA (ncRNA), newly recognized players in transcriptional regulation. This high percentage of non-coding sequences is reasonable,
as other genomic studies indicate about 50% of an organism’s RNA is non-coding. Our average non-coding sequence length was 600nt, significantly longer than our average Artemia 3’UTR length of 175nt, which can easily be explained if we acknowledge these sequences as long non-coding RNAs. Many of our non-coding RNAs also contain polyA tails, as well as polyadenylation signals. Considering many ncRNAs are polyadenylated, this data supports my hypothesis. Fifty-two percent of our non-coding sequences match
other Artemia sequences in NCBI, and of these matches, 33% are in the reverse direction. Transcription in the reverse direction is a method used by ncRNA to inhibit gene transcription.
In addition to my analysis of the 628 analyzed Artemia sequences, I used DNASTAR software to analyze all 5,947 Artemia sequences generated from 2005 through 2008. This software validated sequence quality and assembled similar sequences into 2,848 contiguous sequences. These contiguous sequences were further processed using Blast2GO, a gene ontology tool, where only 268 contiguous sequences were of high
enough quality to be considered annotated genes. These genes were further characterized according to their Gene Ontology.
as other genomic studies indicate about 50% of an organism’s RNA is non-coding. Our average non-coding sequence length was 600nt, significantly longer than our average Artemia 3’UTR length of 175nt, which can easily be explained if we acknowledge these sequences as long non-coding RNAs. Many of our non-coding RNAs also contain polyA tails, as well as polyadenylation signals. Considering many ncRNAs are polyadenylated, this data supports my hypothesis. Fifty-two percent of our non-coding sequences match
other Artemia sequences in NCBI, and of these matches, 33% are in the reverse direction. Transcription in the reverse direction is a method used by ncRNA to inhibit gene transcription.
In addition to my analysis of the 628 analyzed Artemia sequences, I used DNASTAR software to analyze all 5,947 Artemia sequences generated from 2005 through 2008. This software validated sequence quality and assembled similar sequences into 2,848 contiguous sequences. These contiguous sequences were further processed using Blast2GO, a gene ontology tool, where only 268 contiguous sequences were of high
enough quality to be considered annotated genes. These genes were further characterized according to their Gene Ontology.
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electronic resource
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ix, 62 p. : ill.
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M.S.
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Includes bibliographical references (p. 60-62)
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by Stacey Lynn Wittig
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Wittig
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Stacey Lynn
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1979-
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Stacey Lynn Wittig
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Vershon
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Andrew
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Andrew K Vershon
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Michael
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Todd
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Todd P Michael
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Gunderson
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Samuel
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Samuel Gunderson
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Rutgers University
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Graduate School - New Brunswick
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2009
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2009-10
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xx
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Rutgers University Electronic Theses and Dissertations
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ETD
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Graduate School - New Brunswick Electronic Theses and Dissertations
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doi:10.7282/T3X92BF9
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ETD graduate
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The author owns the copyright to this work
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Open
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Wittig
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Stacey
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Stacey Wittig
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Rutgers University. Graduate School - New Brunswick
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I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
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