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Evolution of individual genes of Sugarcane mosaic virus

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TitleInfo
Title
Evolution of individual genes of Sugarcane mosaic virus
Name (type = personal)
NamePart (type = family)
Njagi
NamePart (type = given)
Chris
NamePart (type = date)
1977-
DisplayForm
Chris Njagi
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Duffy
NamePart (type = given)
Siobain
DisplayForm
Siobain Duffy
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2018
DateOther (qualifier = exact); (type = degree)
2018-10
CopyrightDate (encoding = w3cdtf)
2018
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Sugarcane mosaic virus (SCMV) belongs to the Potyvirus genus and Potyviridae family of single-stranded RNA viruses. It is a disease of great economic importance, especially in sugarcane and maize in many parts of the world. SCMV has been understudied at both the genomic level with a greater emphasis put on the coat protein gene (CP) for molecular epidemiology. This was a computational study using publicly available sequences (NCBI GenBank) that sought to understand the evolutionary processes that shape SCMV molecular evolution such as phylogeny, recombination, selection pressure and nucleotide diversity by focusing on the individual genes of the polypeptide. Recombination was found to be a major driver of evolution with breakpoints found in P3, HC-Pro, C1, NIa-Pro, NIb, and CP. No statistically significant recombination was detected in the P1, 6K1, 6K2, and VPg genes most probably because of their relatively shorter length. After the removal of recombinants from the initial 82 full polyprotein-coding sequences, 57 sequences were used in phylogenetic analysis using a Bayesian MCMC framework implemented in BEAST2 with particular substitution models for each gene. All the ten genes gave similar low mean nucleotide substitution rates of between 3.35 x 10-3 (C1) to 4.29 x 10-3 (CP) and time to the most recent common ancestor (TMRCA) of 219 years (CP) to 264 years (P1). This would mean that the community’s over-reliance on the CP may produce results accurate for the whole genome, provided the researchers controlled for the effects of recombination, but that sufficient data exists for other genes as well, so there is no rational justification for excluding them from similar studies. The SCMV strains clustered into two distinct groups with sub-clustering well defined by their geographical isolation points, with sequences from Argentina closely grouping with Chinese strains. This observation may not be conclusive as most of the sequences studied were from China. Analysis of dN/dS shows significant negative selection in all the genes with P1 and CP registering relatively lower levels (SLAC: 0.192 for P1 and 0.153 for CP). A few sites in P1, HC-Pro, P3, NIa-VP, NIb, and CP appear to be under diversifying selection. P1 and CP also had the highest nucleotide diversity while the overlapping P3N-PIPO region had the least diversity relative to other regions of the polypeptide. The overlapping region is understandably highly conserved and presumably under strong purifying selection due to its double role in translation. This knowledge from this study enhances the understanding of SCMV evolution, highlights residues in several genes that may be affecting SCMV-crop interactions and will help in developing strategies for the control of the diseases in plants.
Subject (authority = RUETD)
Topic
Cell and Developmental Biology
Subject
Topic
Sugarcane mosaic virus--Genetic aspects
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_9150
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (61 pages) : illustrations
Note (type = degree)
M.S.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Chris Njagi
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/t3-nxy1-wm61
Genre (authority = ExL-Esploro)
ETD graduate
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Njagi
GivenName
Chris
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2018-08-21 02:43:13
AssociatedEntity
Name
Chris Njagi
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
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.
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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1.7
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DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2018-08-22T13:57:01
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2018-08-22T13:57:01
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