Genome-wide analysis of transcriptome dynamics in plants and algae

Genome-wide analysis of transcriptome dynamics in plants and algae

Bibliographic Details
Main Author: Zhao, Zhixin
Language:English
Published: Miami University / OhioLINK 2013
Subjects:
Bioinformatics
Polyadenylation
splicing
plants
algae
tandem repeats
phytozome
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=miami1385672751
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-miami13856727512021-08-03T06:20:51Z Genome-wide analysis of transcriptome dynamics in plants and algae Zhao, Zhixin Bioinformatics Polyadenylation splicing plants algae tandem repeats phytozome Genome-wide transcriptome analysis is a prevalent research field. The first chapter gives a mini review on polyadenylation in plants and algae. The second chapter illuminates newly detected putative poly(A) signals (UAA and UAAA) in seven species. Based on this systematic analysis of the AAUAAA signal from a wide range of organisms, our results suggest that the first two bases (i.e., NN in NNUAAA) are likely degenerated whereas UAAA appears to be the core part of the motif. Combined with other published results, our comparative poly(A) signal study suggests that AAUAAA may be derived from UAA with an intermediate, putative poly(A) signal of UAAA, following the pathway UAA---UAAA---AAUAAA. The third chapter deeply analyzes poly(A) signals and alternative polyadenylation (APA) utilizing different sequencing data (i.e., ESTs, 454 and Illumina) in green alga Chlamydomonas reinhardtii. In comparison with previous collections, more new poly(A) sites are found in coding sequences (CDS), intron and intergenic regions by deep-sequencing. Prevalence of different poly(A) signal between CDS and 3-UTR might indicate a different mechanism of polyadenylation. Our data analysis suggests that the extent of alternative polyadenylation (APA) is about 68% in C. reinhardtii. Using Gene Ontolgy (GO) analysis, we found most of the APA genes involve in protein synthesis, hydrolase and ligase activates. Moreover, intronic poly(A) sites are more abundant in constitutively spliced introns than the retained introns, suggesting interplay between polyadenylation and splicing.A mini review of Tandem Repeats (TRs) is presented in chapter 4. Chapter 5 characterizes TR motif features and explorers their distributions among 31 plant and green algal species in Phytozome v8.0. It is indicated that genome sizes have no significantly discernable relationship with TR densities, and the highest TR densities are detected in 5-UTRs in land plants and in introns in green algae respectively. GO annotation in two green algae reveals that the genes with TRs in introns are significantly involved in transcriptional and translational processing. Our study shows that TRs display non-random distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae. 2013-12-04 English text Miami University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=miami1385672751 http://rave.ohiolink.edu/etdc/view?acc_num=miami1385672751 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
Polyadenylation
splicing
plants
algae
tandem repeats
phytozome
spellingShingle Bioinformatics
Polyadenylation
splicing
plants
algae
tandem repeats
phytozome
Zhao, Zhixin
Genome-wide analysis of transcriptome dynamics in plants and algae
author Zhao, Zhixin
author_facet Zhao, Zhixin
author_sort Zhao, Zhixin
title Genome-wide analysis of transcriptome dynamics in plants and algae
title_short Genome-wide analysis of transcriptome dynamics in plants and algae
title_full Genome-wide analysis of transcriptome dynamics in plants and algae
title_fullStr Genome-wide analysis of transcriptome dynamics in plants and algae
title_full_unstemmed Genome-wide analysis of transcriptome dynamics in plants and algae
title_sort genome-wide analysis of transcriptome dynamics in plants and algae
publisher Miami University / OhioLINK
publishDate 2013
url http://rave.ohiolink.edu/etdc/view?acc_num=miami1385672751
work_keys_str_mv AT zhaozhixin genomewideanalysisoftranscriptomedynamicsinplantsandalgae
_version_ 1719434964046446592

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