CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING
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Case Western Reserve University School of Graduate Studies / OhioLINK
2012
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| Online Access: | http://rave.ohiolink.edu/etdc/view?acc_num=case1333648149 |
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ndltd-OhioLink-oai-etd.ohiolink.edu-case13336481492021-08-03T05:34:26Z CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING Moss, Tiffanie Bioinformatics Biology Genetics Molecular Biology Plant Biology microRNA miRNA flax linseed bioinformatics computational prediction PAV structural variation genotroph The recent sequencing and assembly of the Bethune genome, a linseed type, and the sequencing of several of the genotrophs of Stormont cirrus, a fiber type, provided a platform for analysis of structural variation sites between flax fiber and linseed types which could be used to identify regions worthy of investigation for the improvement of seed and fiber traits in flax. The most well characterized site of structural variation in flax is that of LIS-1, an environmentally inducible and heritable 5.7Kb structural variation. Previous investigations suggest the LIS-1 structural variant is the result of a programmed DNA rearrangement. The only vaguely comparable system for controlled or programmed DNA rearrangement is that seen in the ciliate macronucleus. The scnRNA mechanism used by ciliates utilizes much of the same machinery as that of small RNAs and the action is similar to that of heterochromatin-associated siRNAs. By identifying small RNAs which map to other regions of structural variation in flax, the impact these regions could have on the microRNA regulated biological pathways, and association of other small RNAs mapping to these regions may be discerned and used to prioritize structural variants for further molecular investigation. Regions of the Bethune genome which may be associated with small RNAs was determined by computational prediction of microRNAs and mapping of small RNA reads from high throughput RNA sequencing. Over 25,000 miRNAs were predicted from the flax genome and Unigene database using the novoMIR plant miRNA prediction program. Of these 649 discreet miRNA gene units were identified as having potential targets among the 30,649 flax Unigenes. RNAseq provided preliminary support for 349 of the predicted miRNAs derived from novoMIR and identified an additional 1.4 million unique reads to be included in further investigations. Sequence similarity to public miRNA databases suggest that the flax transcriptome utilizes most of the conserved miRNAs among angiosperm and will likely have similar regulatory roles. Using Perl programming scripts, 44,106 PAV sites of at least 1Kb were identified between flax linseed and fiber types. 143 PAV sites were found to be associated with computationally predicted miRNAs or sRNAs identified by high-throughput sequencing. 2012-06-26 English text Case Western Reserve University School of Graduate Studies / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=case1333648149 http://rave.ohiolink.edu/etdc/view?acc_num=case1333648149 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws. |
| collection |
NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Bioinformatics Biology Genetics Molecular Biology Plant Biology microRNA miRNA flax linseed bioinformatics computational prediction PAV structural variation genotroph |
| spellingShingle |
Bioinformatics Biology Genetics Molecular Biology Plant Biology microRNA miRNA flax linseed bioinformatics computational prediction PAV structural variation genotroph Moss, Tiffanie CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| author |
Moss, Tiffanie |
| author_facet |
Moss, Tiffanie |
| author_sort |
Moss, Tiffanie |
| title |
CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| title_short |
CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| title_full |
CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| title_fullStr |
CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| title_full_unstemmed |
CHARACTERIZATION OF STRUCTURAL VARIANTS AND ASSOCIATED MICRORNAS IN FLAX FIBER AND LINSEED GENOTYPES BY BIOINFORMATIC ANALYSIS AND HIGH-THROUGHPUT SEQUENCING |
| title_sort |
characterization of structural variants and associated micrornas in flax fiber and linseed genotypes by bioinformatic analysis and high-throughput sequencing |
| publisher |
Case Western Reserve University School of Graduate Studies / OhioLINK |
| publishDate |
2012 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=case1333648149 |
| work_keys_str_mv |
AT mosstiffanie characterizationofstructuralvariantsandassociatedmicrornasinflaxfiberandlinseedgenotypesbybioinformaticanalysisandhighthroughputsequencing |
| _version_ |
1719421938828312576 |