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Genomics and transcriptomics of the greater duckweed, Spirodela polyrhiza, a model for aquatic biology
Descriptive
TitleInfo
Title
Genomics and transcriptomics of the greater duckweed, Spirodela polyrhiza, a model for aquatic biology
Name
(type = personal)
NamePart
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Wang
NamePart
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Wenqin
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Wenqin Wang
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author
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(type = personal)
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(type = family)
Messing
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Joachim
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Joachim Messing
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Advisory Committee
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chair
Name
(type = personal)
NamePart
(type = family)
Dooner
NamePart
(type = given)
Hugo K.
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Hugo K. Dooner
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Advisory Committee
Role
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internal member
Name
(type = personal)
NamePart
(type = family)
Maliga
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(type = given)
Pal
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Pal Maliga
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Advisory Committee
Role
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(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Du
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(type = given)
Chunguang
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Chunguang Du
Affiliation
Advisory Committee
Role
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outside member
Name
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NamePart
Rutgers University
Role
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(authority = RULIB)
degree grantor
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NamePart
Graduate School - New Brunswick
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school
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Text
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theses
OriginInfo
DateCreated
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2014
DateOther
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(type = degree)
2014-01
Place
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xx
Language
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(type = code)
eng
Abstract
(type = abstract)
My thesis provides the first whole genome analysis of an aquatic plant, Spirodela polyrhiza and a reference genome for a new order among the monocotelydonous angiosperms. The Lemnoideae belong to the order of the Alismatales and are commonly known as duckweeds, the smallest, fastest growing, and simplest of aquatic plants, thus telling them apart is not a trivial task. Whereas a simple and accessible protocol has been established for land plants by the Consortium for the Barcode of Life with seven universal DNA barcoding markers, we found that atpF-atpH noncoding spacer is the most promising marker for duckweed species-level identification. Furthermore, our assembly and annotation of the Spirodela chloroplast and mitochondrial genomes open an opportunity of population-level classification. A key to our understanding of the evolution of a species and its potential use is the gene content of the organism. Therefore, we sequenced Spirodela polyrhiza 7498 that has one of the smallest genomes with 158 Mb within this subfamily of species. The genome contains 19,623 predicted protein-coding genes, sharing a total of 8,255 common gene families with Arabidopsis, tomato, banana, and rice despite a significantly reduced gene number. Reduced gene families and missing genes reflect changes consistent with its compact and reduced morphogenesis or forever-young life style, aquatic suspension, and suppression of juvenile-to-adult transition. Spirodela exhibits a remarkable phenotypic plasticity to adapt to cold weather in winter. We identified and functionally annotated 362 differentially expressed genes, which open a major step towards understanding the molecular network underlying vegetative frond dormancy. Moreover, the expression data for lipid and starch biosynthesis together with the turion-specific transcriptional genes from our RNA-Seq data could be ideal targets to develop duckweeds into oil crops. Thanks to its unique and fascinating biology, applications of duckweed in water remediation and as a renewable energy source are predicted to have a bright future. The genome sequence of Spirodela provides the first step to identify, understand, and improve relevant traits for specific target applications.
Subject
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Topic
Plant Biology
RelatedItem
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
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ETD
Identifier
ETD_5223
PhysicalDescription
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electronic resource
InternetMediaType
application/pdf
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text/xml
Extent
xii, 349 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Wenqin Wang
Subject
(authority = ETD-LCSH)
Topic
Duckweeds
Subject
(authority = ETD-LCSH)
Topic
Genomics
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
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rucore19991600001
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NjNbRU
Identifier
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doi:10.7282/T3GH9G18
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
RightsDeclaration
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The author owns the copyright to this work.
RightsHolder
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Name
FamilyName
Wang
GivenName
Wenqin
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
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(point = start)
2013-12-18 14:22:32
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Name
Wenqin Wang
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
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.
RightsEvent
DateTime
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(qualifier = exact);
(point = start)
2014-01-31
DateTime
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2014-08-02
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after August 2nd, 2014.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical
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ETD
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windows xp
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