Relevant bibliographies by topics / Comparative Genomics Analysis

Academic literature on the topic 'Comparative Genomics Analysis'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Comparative Genomics Analysis"

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Alam, Intikhab, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, and Norman W. Paton. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 2007): 112–22. http://dx.doi.org/10.1515/jib-2007-69.

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Abstract The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.
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LAKE, J. "Phylogenetic analysis and comparative genomics." Trends in Biotechnology 16 (November 1998): 22–23. http://dx.doi.org/10.1016/s0167-7799(98)00132-2.

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Holmer, Rens, Robin van Velzen, Rene Geurts, Ton Bisseling, Dick de Ridder, and Sandra Smit. "GeneNoteBook, a collaborative notebook for comparative genomics." Bioinformatics 35, no. 22 (June 14, 2019): 4779–81. http://dx.doi.org/10.1093/bioinformatics/btz491.

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Abstract Summary Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. Availability and implementation GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. Supplementary information Supplementary data are available at Bioinformatics online.
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Valentin, Guignon, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Conte Matthieu, and Rouard Mathieu. "GreenPhylDB v5: a comparative pangenomic database for plant genomes." Nucleic Acids Research 49, no. D1 (November 25, 2020): D1464—D1471. http://dx.doi.org/10.1093/nar/gkaa1068.

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Abstract Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.
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Blanca, Léo, Eugène Christo-Foroux, Sofia Rigou, and Matthieu Legendre. "Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes." Viruses 12, no. 11 (November 7, 2020): 1270. http://dx.doi.org/10.3390/v12111270.

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Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.
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Dodeweerd, Anne-Marie van, Caroline R. Hall, Elisabeth G. Bent, Samantha J. Johnson, Michael W. Bevan, and Ian Bancroft. "Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana." Genome 42, no. 5 (October 1, 1999): 887–92. http://dx.doi.org/10.1139/g99-033.

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Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.
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Peng, Qin, Yihui Yuan, Meiying Gao, Xupeng Chen, Biao Liu, Pengming Liu, Yan Wu, and Dandan Wu. "Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25." BMC Genomics 15, no. 1 (2014): 144. http://dx.doi.org/10.1186/1471-2164-15-144.

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Liu, J. "Genomic resources and their informatic analysis for comparative genomics in catfish." Aquaculture 272 (2007): S286. http://dx.doi.org/10.1016/j.aquaculture.2007.07.128.

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Koike, Hideaki, Andrea Aerts, Kurt LaButti, Igor V. Grigoriev, and Scott E. Baker. "Comparative Genomics Analysis of Trichoderma reesei Strains." Industrial Biotechnology 9, no. 6 (December 2013): 352–67. http://dx.doi.org/10.1089/ind.2013.0015.

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Leiting, W. U., and X. I. E. Jianping. "Comparative genomics analysis of Mycobacterium NrdH-redoxins." Microbial Pathogenesis 48, no. 3-4 (March 2010): 97–102. http://dx.doi.org/10.1016/j.micpath.2010.01.004.

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Dissertations / Theses on the topic "Comparative Genomics Analysis"

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Prakash, Amol. "Algorithms for comparative sequence analysis and comparative proteomics /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6904.

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Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.

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Jordan, Gregory. "Analysis of alignment error and sitewise constraint in mammalian comparative genomics." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610693.

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Jentzsch, Iris Miriam Vargas. "Comparative genomics of microsatellite abundance: a critical analysis of methods and definitions." Thesis, University of Canterbury. Biological Sciences, 2009. http://hdl.handle.net/10092/4282.

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This PhD dissertation is focused on short tandemly repeated nucleotide patterns which occur extremely often across DNA sequences, called microsatellites. The main characteristic of microsatellites, and probably the reason why they are so abundant across genomes, is the extremely high frequency of specific replication errors occurring within their sequences, which usually cause addition or deletion of one or more complete tandem repeat units. Due to these errors, frequent fluctuations in the number of repetitive units can be observed among cellular and organismal generations. The molecular mechanisms as well as the consequences of these microsatellite mutations, both, on a generational as well as on an evolutionary scale, have sparked debate and controversy among the scientific community. Furthermore, the bioinformatic approaches used to study microsatellites and the ways microsatellites are referred to in the general literature are often not rigurous, leading to misinterpretations and inconsistencies among studies. As an introduction to this complex topic, in Chapter I I present a review of the knowledge accumulated on microsatellites during the past two decades. A major part of this chapter has been published in the Encyclopedia of Life Sciences in a Chapter about microsatellite evolution (see Publication 1 in Appendix II). The ongoing controversy about the rates and patterns of microsatellite mutation was evident to me since before starting this PhD thesis. However, the subtler problems inherent to the computational analyses of microsatellites within genomes only became apparent when retrieving information on microsatellite distribution and abundance for the design of comparative genomic analyses. There are numerous publications analyzing the microsatellite content of genomes but, in most cases, the results presented can neither be reliably compared nor reproduced, mainly due to the lack of details on the microsatellite search process (particularly the program’s algorithm and the search parameters used) and because the results are expressed in terms that are relative to the search process (i.e. measures based on the absolute number of microsatellites). Therefore, in Chapter II I present a critical review of all available software tools designed to scan DNA sequences for microsatellites. My aim in undertaking this review was to assess the comparability of search results among microsatellite programs, and to identify the programs most suitable for the generation of microsatellite datasets for a thorough and reproducible comparative analysis of microsatellite content among genomic sequences. Using sequence data where the number and types of microsatellites were empirical know I compared the ability of 19 programs to accurately identify and report microsatellites. I then chose the two programs which, based on the algorithm and its parameters as well as the output informativity, offered the information most suitable for biological interpretation, while also reflecting as close as possible the microsatellite content of the test files. From the analysis of microsatellite search results generated by the various programs available, it became apparent that the program’s search parameters, which are specified by the user in order to define the microsatellite characteristics to the program, influence dramatically the resulting datasets. This is especially true for programs suited to allow imperfections within tandem repeats, because imperfect repetitions can not be defined accurately as is the case for perfect ones, and because several different algorithms have been proposed to address this problem. The detection of approximate microsatellites is, however, essential for the study of microsatellite evolution and for comparative analyses based on microsatellites. It is now well accepted that small deviations from perfect tandem repeat structure are common within microsatellites and larger repeats, and a number of different algorithms have been developed to confront the challenge of finding and registering microsatellites with all expectable kinds of imperfection. However, biologists have still to apply these tools to their full potential. In biological analyses single tandem repeat hits are consistently interpreted as isolated and independent repeats. This interpretation also depends on the search strategy used to report the microsatellites in DNA sequences and, therefore, I was particularly interested in the capacity of repeat finding programs to report imperfect microsatellites allowing interpretations that are useful in a biological sense. After analzying a series of tandem repeat finding programs I optimized my microsatellite searches to yield the best possible datasets for assessing and comparing the degree of imperfection of microsatellites among different genomes (Chapter III) During the program comparisons performed in Chapter II, I show that the most critical search parameter influencing microsatellite search results is the minimum length threshold. Biologically speaking, there is no consensus with respect to the minimum length, beyond which a short tandem repeat is expected to become prone to microsatellite-like mutations. Usually, a single absolute value of ~12 nucleotides is assigned irrespective of motif length.. In other cases thresholds are assigned in terms of number of repeat units (i.e. 3 to 5 repeats or more), which are better applied individually for each motif. The variation in these thresholds is considerable and not always justifiable. In addition, any current minimum length measures are likely naïve because it is clear that different microsatellite motifs undergo replication slippage at different length thresholds. Therefore, in Chapter III, I apply two probabilistic models to predict the minimum length at which microsatellites of varying motif types become overrepresented in different genomes based on the individual oligonucleotide frequency data of these genomes. Finally, after a range of optimizations and critical analyses, I performed a preliminary analysis of microsatellite abundance among 24 high quality complete eukaryotic genomes, including also 8 prokaryotic and 5 archaeal genomes for contrast. The availability of the methodologies and the microsatellite datasets generated in this project will allow informed formulation of questions for more specific genome research, either about microsatellites, or about other genomic features microsatellites could influence. These datasets are what I would have needed at the beginning of my PhD to support my experimental design, and are essential for the adequate data interpretation of microsatellite data in the context of the major evolutionary units; chromosomes and genomes.
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Chen, Lu. "Comparative and functional analysis of alternative splicing in eukaryotic genomes." Thesis, University of Bath, 2012. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.558885.

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Alternative splicing (AS) is a common post-transcriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. Because of its potential role in expanding transcript diversity, interest in alternative splicing has been increasing over the last decade, ever since the release of the human genome draft showed it contained little more than the number of genes of a worm. Although recent studies have shown that 94% human multi-exon genes undergo AS while aberrant AS may cause disease or cancer, evolution of AS in eukaryotic genomes remains largely unexplored mainly due to the lack of comparable AS estimates. In this thesis I built a Eukaryote Comprehensive & Comparable Alternative Splicing Events Database (ECCASED) based on the analyses of over 30 million Expressed Sequence Tag (ESTs) for 114 eukaryotic genomes, including protists (22), plants (20), fungi (23), metazoan (non-vertebrates, 29) and vertebrates (20). Using this database, I addressed two main questions: 1) How does alternative splicing relate to gene duplication (GD) as an alternative mechanism to increase transcript diversity? and 2) What is the contribution of alternative splicing to eukaryote transcript diversity? I found that the previous “interchangeable model” of AS and gene duplication is a by-product of an existing relation between gene expression breadth, AS and gene family size. I also show that alternative splicing has played a key role in the expansion of transcript diversity and that this expansion is the best predictor reported to date of organisms complexity assayed as number of cell types. In addition, by comparing alternative splicing patterns in cancer and normal transcript libraries I found that cancer derived transcript libraries have increased levels of “noisy splicing”.
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Nelson, A. D. L., E. S. Forsythe, U. K. Devisetty, D. S. Clausen, A. K. Haug-Batzell, A. M. R. Meldrum, M. R. Frank, E. Lyons, and M. A. Beilstein. "A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants." GENETICS SOCIETY AMERICA, 2016. http://hdl.handle.net/10150/621708.

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Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of >5000 lincRNA loci from A. thaliana. From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.
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Jiang, Xiaofang. "Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/79959.

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Anopheles stephensi is a potent vector of malaria throughout the Indian subcontinent and Middle East. An. stephensi is emerging as a model for molecular and genetic studies of mosquito-parasite interactions. Here we conducted a series of genomic and transcriptomic studies to improve the understanding of the biology of Anopheles stephensi and mosquito in general. First we reported the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly was produced using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than assemblies generated from a single data source. A total of 11,789 protein-encoding genes were annotated using a combination of homology and de novo prediction. Secondly, we demonstrated the presence of complete dosage compensation in An. stephensi by determining that autosomal and X-linked genes have very similar levels of expression in both males and females. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the conclusion of complete dosage compensation in Anopheles. Lastly, we investigated trans-splicing events in Anopheles stephensi. We identified six trans-splicing events and all the trans-splicing sites are conserved and present in Ae. aegypti. The proteins encoded by the trans-spliced mRNAs are also highly conserved and their orthologs are co-linearly transcribed in out-groups of family Culicidae. This finding indicates the need to preserve the intact mRNA and protein function of the broken-up genes by trans-splicing during evolution. In summary, we presented the first genome assembly of Anopheles stephensi and studied two interesting evolution events" dosage compensation and trans-splicing - via transcriptomic analysis.
Ph. D.
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Motro, Yair. "Comparative genomics analysis and development of bioinformatics tools for two newly sequenced spirochaete species." Thesis, Motro, Yair (2008) Comparative genomics analysis and development of bioinformatics tools for two newly sequenced spirochaete species. PhD thesis, Murdoch University, 2008. https://researchrepository.murdoch.edu.au/id/eprint/41679/.

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The bacterial family Spirochaetales contains a number of potent pathogens responsible for serious and well-known diseases, such as tick Lyme disease (Borrelia burgdoferri), leptospirosis (Leptospira interrogens), and sypillis (Treponema pallidum). Though the mentioned species have been extensively investigated, there still remain spirochaete genera, and the spirochaete family as a whole, that have been minimally characterised. The Brachyspira genera includes species primarily responsible for gastro-intestinal diseases. Some biological characteristics of the two species B. hyodysenteriae and B. pilosicoli are known. For example B. hyodysenteriae causes disease in swine, while B. pilosicoli causes disease in a wide range of animals and humans. As there are no whole genome sequences available for any Brachyspira species, their underlying molecular mechanisms, evolution and function are not understood. This work is part of a large project which aims to sequence the two whole genome sequences for vaccine design and development. This thesis represents the first report of an in-depth comparative genome analysis (CGA) of the novel whole genome sequences of both Brachyspira species, providing greater understanding into their genomic functional relationships, evolution and diversity, while also identifying elements for potential vaccine and drug design and development.
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Sturgill, David Matthew. "Comparative Genome Analysis of Three Brucella spp. and a Data Model for Automated Multiple Genome Comparison." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/10163.

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Comparative analysis of multiple genomes presents many challenges ranging from management of information about thousands of local similarities to definition of features by combination of evidence from multiple analyses and experiments. This research represents the development stage of a database-backed pipeline for comparative analysis of multiple genomes. The genomes of three recently sequenced species of Brucella were compared and a superset of known and hypothetical coding sequences was identified to be used in design of a discriminatory genomic cDNA array for comparative functional genomics experiments. Comparisons were made of coding regions from the public, annotated sequence of B. melitensis (GenBank) to the annotated sequence of B. suis (TIGR) and to the newly-sequenced B. abortus (personal communication, S. Halling, National Animal Disease Center, USDA). A systematic approach to analysis of multiple genome sequences is described including a data model for storage of defined features is presented along with necessary descriptive information such as input parameters and scores from the methods used to define features. A collection of adjacency relationships between features is also stored, creating a unified database that can be mined for patterns of features which repeat among or within genomes. The biological utility of the data model was demonstrated by a detailed analysis of the multiple genome comparison used to create the sample data set. This examination of genetic differences between three Brucella species with different virulence patterns and host preferences enabled investigation of the genomic basis of virulence. In the B. suis genome, seventy-one differentiating genes were found, including a contiguous 17.6 kb region unique to the species. Although only one unique species-specific gene was identified in the B. melitensis genome and none in the B. abortus genome, seventy-nine differentiating genes were found to be present in only two of the three Brucella species. These differentiating features may be significant in explaining differences in virulence or host specificity. RT-PCR analysis was performed to determine whether these genes are transcribed in vitro. Detailed comparisons were performed on a putative B. suis pathogenicity island (PAI). An overview of these genomic differences and discussion of their significance in the context of host preference and virulence is presented.
Master of Science
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McAdam, Paul R. "Population analysis of bacterial pathogens on distinct temporal and spatial scales." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/17852.

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Bacteria have been the causative agents of major infectious disease pandemics throughout human history. Over the past 4 decades, a combination of changing medical practices, industrialization, and globalisation have led to a number of emergences and re-emergences of bacterial pathogens. The design of rational control programs and bespoke therapies will require an enhanced understanding of the dynamics underpinning the emergence and transmission of pathogenic clones. The recent development of new technologies for sequencing bacterial genomes rapidly and economically has led to a greatly enhanced understanding of the diversity of bacterial populations. This thesis describes the application of whole genome sequencing of 2 bacterial pathogens, Staphylococcus aureus and Legionella pneumophila, in order to understand the dynamics of bacterial infections on different temporal and spatial scales. The first study involves the examination of S. aureus evolution during a chronic infection of a single patient over a period of 26 months revealing differences in antibiotic resistance profiles and virulence factor expression over time. The genetic variation identified correlated with differences in growth rate, haemolytic activity, and antibiotic sensitivity, implying a profound effect on the ecology of S. aureus. Importantly, polymorphisms were identified in global regulators of virulence, with a high frequency of polymorphisms within the SigB locus identified, suggesting this region may be under selection in this patient. The identification of genes under diversifying selection during long-term infection may inform the design of novel therapeutics for the control of refractory chronic infections. Secondly, the emergence and transmission of 3 pandemic lineages derived from S. aureus clonal complex 30 (CC30) were investigated. Independent origins for each pandemic lineage were identified, with striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements, such as bacteriophage and Staphylococcal pathogenicity islands, and non-synonymous mutations affecting antibiotic resistance and virulence. Hospitals in large cities were identified as hubs for the transmission of MRSA to regional health care centres. In addition, comparison of whole genome sequences revealed that at least 3 independent acquisitions of TSST-1 have occurred in CC30, but a single distinct clade of diverse community-associated CC30 strains was responsible for the TSS epidemic of the late 1970s, and for subsequent cases of TSS in the UK and USA. Finally, whole genome sequencing was used as a tool for investigating a recent outbreak of legionellosis in Edinburgh. An unexpectedly high level of genomic diversity was identified among the outbreak strains, with respect to core genome polymorphisms, and accessory genome content. The data indicate that affected individuals may be infected with heterogeneous strains. The findings highlight the complexities in identifying environmental sources and suggest possible differences in pathogenic potential among isolates from a single outbreak. Taken together, the findings demonstrate applications of bacterial genome sequencing leading to enhanced understanding of bacterial pathogen evolution, emergence, and transmission, which may ultimately inform appropriate infection control measures.
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Books on the topic "Comparative Genomics Analysis"

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H, Bergman Nicholas, ed. Comparative genomics. Totowa, NJ: Humana Press, 2007.

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Foundations of comparative genomics. Boston, MA: Elsevier Academic Press, 2006.

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Per, Sunnerhagen, and Piškur Jure, eds. Comparative genomics: Using fungi as models. Berlin: Springer, 2006.

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Handbook of comparative genomics: Principles and methodology. Hoboken, NJ: Wiley-Liss, 2002.

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Y, Galperin Michael, ed. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Koonin, Eugene V. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Koonin, Eugene V. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Moller, Maria. Comparative genome analysis in the pig. Uppsala: Sveriges Lantbruksuniversitet, 1995.

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Morgunova, Elena, and Beniamin Shahnazarov. Intellectual property law in the context of the development of new technologies. ru: INFRA-M Academic Publishing LLC., 2022. http://dx.doi.org/10.12737/1905571.

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The monograph is devoted to the problems of providing legal protection to the results of intellectual activity and means of individualization, their use and protection of rights to them in the context of modern challenges associated with the development of new information technologies, artificial intelligence, genomic technologies, etc. Considerable attention is paid to the comparative analysis of the legal regulation of these relations. The publication is addressed to scientists, teachers, graduate students, law students and anyone interested in intellectual property issues.
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Mushegian, Arcady R. Foundations of Comparative Genomics. Elsevier Science & Technology Books, 2010.

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Book chapters on the topic "Comparative Genomics Analysis"

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Touzet, Hélène. "Comparative Analysis of RNA Genes." In Comparative Genomics, 465–73. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-514-5_29.

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Zekic, Tina, Guillaume Holley, and Jens Stoye. "Pan-Genome Storage and Analysis Techniques." In Comparative Genomics, 29–53. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_2.

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Chin, Lung Lu, Chih Lin Ying, Lin Huang Yen, and Yi Tang Chuan. "Analysis of Genome Rearrangement by Block-Interchanges." In Comparative Genomics, 121–34. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2_9.

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Hsu, Chih-Hao, Yu Zhang, Ross Hardison, and Webb Miller. "Whole-Genome Analysis of Gene Conversion Events." In Comparative Genomics, 181–92. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04744-2_15.

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Amgarten, Deyvid, and Chris Upton. "Bioinformatic Approaches for Comparative Analysis of Viruses." In Comparative Genomics, 401–17. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_15.

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Karolchik, Donna, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb Miller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, and W. James Kent. "Comparative Genomic Analysis Using the UCSC Genome Browser." In Comparative Genomics, 17–33. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-514-5_2.

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Caprara, Alberto, and Giuseppe Lancia. "Experimental and Statistical Analysis of Sorting by Reversals." In Comparative Genomics, 171–83. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4309-7_16.

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Doerr, Daniel, and Bernard M. E. Moret. "Sequence-Based Synteny Analysis of Multiple Large Genomes." In Comparative Genomics, 317–29. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_11.

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Moura, Gabriela, Miguel Pinheiro, Adelaide Valente Freitas, José Luís Oliveira, and Manuel A. S. Santos. "Computational and Statistical Methodologies for ORFeome Primary Structure Analysis." In Comparative Genomics, 449–62. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-514-5_28.

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Sankoff, David, and Chunfang Zheng. "Whole Genome Duplication in Plants: Implications for Evolutionary Analysis." In Comparative Genomics, 291–315. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_10.

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Conference papers on the topic "Comparative Genomics Analysis"

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DUBCHAK, INNA, LIOR PACHTER, and LIPING WEI. "GENOME-WIDE ANALYSIS AND COMPARATIVE GENOMICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0011.

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V. S., Muntyan, Kozlova A. P., Afonin A. M., Muntyan A. N., Dzyubenko E. A., Kabilov M.R., Antonova E. V., and Roumiantseva M. L. "Comparative Genomic Analysis of Moderate Bacteriophages of Alfalfa Root Nodule Bacteria." In 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB). IEEE, 2020. http://dx.doi.org/10.1109/csgb51356.2020.9214723.

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Whalen, Sean, and Gaurav Pandey. "A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics." In 2013 IEEE International Conference on Data Mining (ICDM). IEEE, 2013. http://dx.doi.org/10.1109/icdm.2013.21.

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"Comparative transcriptome analysis of Syringa vulgaris vegetative apices in vivo and in vitro." In Current Challenges in Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences Novosibirsk State University, 2019. http://dx.doi.org/10.18699/icg-plantgen2019-53.

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Kashtanov, Aleksandr A., Mihail E. Pazhetnov, and Elena V. Kashtanova. "Comparative Analysis of the Types of Processing of Visual Information from the Point of View of Cognitive Science." In 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB). IEEE, 2020. http://dx.doi.org/10.1109/csgb51356.2020.9214772.

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"The comparative plastome analysis of twelve Allium species: adaptation to shaded environments could be accompanied by the complete loss function of the NDH genes." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-183.

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Geib, Scott. "Comparative genomics of tephritid fruit flies: Strategies and approaches in genome sequencing and analysis." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.113075.

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"Analysis of environment adaptation features of the bacteria of Flavobacterium genus by comparative genomics." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-086.

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Liu, Jun, Sanjay Ranka, Tamer Kahveci, Onur Seref, O. Erhun Kundakcioglu, and Panos Pardalos. "A web server for mining Comparative Genomic Hybridization (CGH) data." In DATA MINING, SYSTEMS ANALYSIS AND OPTIMIZATION IN BIOMEDICINE. AIP, 2007. http://dx.doi.org/10.1063/1.2817337.

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Kakumani, Rajasekhar, M. Omair Ahmad, and Vijay Devabhaktunit. "Comparative genomic analysis using statistically optimal null filters." In 2010 IEEE International Symposium on Circuits and Systems - ISCAS 2010. IEEE, 2010. http://dx.doi.org/10.1109/iscas.2010.5537210.

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Reports on the topic "Comparative Genomics Analysis"

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Qiu, D., Q. Tu, Zhili He, and Jizhong Zhou. Comparative Genomics Analysis and Phenotypic Characterization of Shewanella putrefaciens W3-18-1: Anaerobic Respiration, Bacterial Microcompartments, and Lateral Flagella. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/986497.

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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.

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Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.
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Zhang, Hongbin, Shahal Abbo, Weidong Chen, Amir Sherman, Dani Shtienberg, and Frederick Muehlbauer. Integrative Physical and Genetic Mapping of the Chickpea Genome for Fine Mapping and Analysis of Agronomic Traits. United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7592122.bard.

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Chickpea is the third most important pulse crop in the world and ranks first in the Middle East; however, it has been subjected to only limited research in modern genomics. In the first period of this project (US-3034-98R) we constructed two large-insert BAC and BIBAC libraries, developed 325 SSR markers and mapped QTLs controlling ascochyta blight resistance (ABR) and days to first flower (DTF). Nevertheless, the utilities of these tools and results in gene discovery and marker-assisted breeding are limited due to the absence of an essential platform. The goals of this period of the project were to use the resources and tools developed in the first period of the project to develop a BAC/BIBAC physical map for chickpea and using it to identify BAC/BIBACcontigs containing agronomic genes of interest, with an emphasis on ABR and DTF, and develop DNA markers suitable for marker-assisted breeding. Toward these goals, we proposed: 1) Fingerprint ~50,000 (10x) BACs from the BAC and BIBAC libraries, assemble the clones into a genome-wide BAC/BIBAC physical map, and integrate the BAC/BIBAC map with the existing chickpea genetic maps (Zhang, USA); 2) fine-map ABR and DTFQTLs and enhance molecular tools for chickpea genetics and breeding (Shahal, Sherman and DaniShtienberg, Israel; Chen and Muehlbauer; USA); and 3) integrate the BAC/BIBAC map with the existing chickpea genetic maps (Sherman, Israel; Zhang and Chen, USA). For these objectives, a total of $460,000 was requested originally, but a total of $300,000 was awarded to the project. We first developed two new BAC and BIBAC libraries, Chickpea-CME and Chickpea- CHV. The chickpea-CMEBAC library contains 22,272 clones, with an average insert size of 130 kb and equivalent to 4.0 fold of the chickpea genome. The chickpea-CHVBIBAC library contains 38,400 clones, with an average insert size of 140 kb and equivalent to 7.5 fold of the chickpea genome. The two new libraries (11.5 x), along with the two BAC (Chickpea-CHI) and BIBAC (Chickpea-CBV) libraries (7.1 x) constructed in the first period of the project, provide libraries essential for chickpea genome physical mapping and many other genomics researches. Using these four libraries we then developed the proposed BAC/BIBAC physical map of chickpea. A total of 67,584 clones were fingerprinted, and 64,211 (~11.6 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBACcontigs, with each containing an average of 39.2 clones and having an average physical length of 559 kb. The contigs collectively span ~1,088 Mb, being 1.49 fold of the 740- Mb chickpea genome. Third, we integrated the physical map with the two existing chickpea genetic maps using a total of 172 (124 + 48) SSR markers. Fourth, we identified tightly linked markers for ABR-QTL1, increased marker density at ABR-QTL2 and studied the genetic basis of resistance to pod abortion, a major problem in the east Mediterranean, caused by heat stress. Finally, we, using the integrated map, isolated the BAC/BIBACcontigs containing or closely linked to QTL4.1, QTL4.2 and QTL8 for ABR and QTL8 for DTF. The integrated BAC/BIBAC map resulted from the project will provide a powerful platform and tools essential for many aspects of advanced genomics and genetics research of this crop and related species. These includes, but are not limited to, targeted development of SNP, InDel and SSR markers, high-resolution mapping of the chickpea genome and its agronomic genes and QTLs, sequencing and decoding of all genes of the genome using the next-generation sequencing technology, and comparative genome analysis of chickpea versus other legumes. The DNA markers and BAC/BIBACcontigs containing or closely linked to ABR and DTF provide essential tools to develop SSR and SNP markers well-suited for marker-assisted breeding of the traits and clone their corresponding genes. The development of the tools and knowledge will thus promote enhanced and substantial genetic improvement of the crop and related legumes.
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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Ramaswamy, Anbazhagan. High Throughput Analysis of the Role of Genomic Methylation in Breast Cancer by Methylation-Sensitive Comparative Genomic Hybridization. Fort Belvoir, VA: Defense Technical Information Center, September 2001. http://dx.doi.org/10.21236/ada397004.

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Markowitz, Victor M., I.-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, et al. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource. Office of Scientific and Technical Information (OSTI), September 2009. http://dx.doi.org/10.2172/980732.

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Mawassi, Munir, and Valerian V. Dolja. Role of the viral AlkB homologs in RNA repair. United States Department of Agriculture, June 2014. http://dx.doi.org/10.32747/2014.7594396.bard.

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AlkB proteins that repair DNA via reversing methylation damage are conserved in a broad range of prokaryotes and eukaryotes including plants. Surprisingly, AlkB-domains were discovered in the genomes of numerous plant positive-strand RNA viruses, majority of which belong to the family Flexiviridae. The major goal of this research was to reveal the AlkB functions in the viral infection cycle using a range of complementary genetic and biochemical approaches. Our hypotheses was that AlkB is required for efficient replication and genetic stability of viral RNA genomes The major objectives of the research were to identify the functions of GVA AlkB domain throughout the virus infection cycle in N. benthamiana and grapevine, to investigate possible RNA silencing suppression activity of the viral AlkBs, and to characterize the RNA demethylation activity of the mutated GVA AlkBs in vitro and in vivo to determine methylation status of the viral RNA. Over the duration of project, we have made a very substantial progress with the first two objectives. Because of the extreme low titer of the virus particles in plants infected with the AlkB mutant viruses, we were unable to analyze RNA demethylation activity and therefore had to abandon third objective. The major achievements with our objectives were demonstration of the AlkB function in virus spread and accumulation in both experimental and natural hosts of GVA, discovery of the functional cooperation and physical interaction between AlkB and p10 AlkB in suppression of plant RNA silencing response, developing a powerful virus vector technology for grapevine using GLRaV-2-derived vectors for functional genomics and pathogen control in grapevine, and in addition we used massive parallel sequencing of siRNAs to conduct comparative analysis of the siRNA populations in grape plants infected with AlkB-containing GLRaV-3 versus GLRaV-2 that does not encode AlkB. This analysis revealed dramatically reduced levels of virus-specific siRNAs in plants infected with GLRaV-3 compared to that in GLRaV-2 infection implicating AlkB in suppression of siRNA formation. We are pleased to report that BARD funding resulted in 5 publications directly supported by BARD, one US patent, and 9 more publications also relevant to project. Moreover, two joint manuscripts that summarize work on GVA AlkB (led by Israeli PI) and on viral siRNAs in grapevine (led by US PI in collaboration with University of Basel) are in preparation.
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Berka, Randy, Igor Grigoriev, Robert Otillar, Asaf Salamov, Jane Grimwood, Ian Reid, Nadeeza Ishmael, et al. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Office of Scientific and Technical Information (OSTI), May 2011. http://dx.doi.org/10.2172/1165279.

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Goodman, David. Comparative Genetic and Genomic Analysis of The Novel Fusellovirus Sulfolobus Spindle-shaped Virus 10. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.6380.

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Jander, Georg, Gad Galili, and Yair Shachar-Hill. Genetic, Genomic and Biochemical Analysis of Arabidopsis Threonine Aldolase and Associated Molecular and Metabolic Networks. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7696546.bard.

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Since the amino acids threonine and isoleucine can be limiting in mammalian diet and there is interest in increasing their abundance in certain crop plants. To meet this need, a BARD proposal was written with two main research objectives: (i) investigate new avenues for manipulating threonine and isoleucine content in plants and (ii) study the role of threonine aldolase in plant metabolism. Research conducted to meet these goals included analysis of the sub-cellular localization of threonine aldolase in the plant, analysis of metabolic flux in developing embryos, over- and under-expression of Arabidopsis threonine aldolases, and transcriptional and metabolic analysis of perturbations resulting from altered threonine aldolase expression. Additionally, the broader metabolic effects of increasing lysine biosynthesis were investigated. An interesting observation that came up in the course of the project is that threonine aldolase activity affects methionine gamma-lyase in Arabidopsis. Further research showed that threonine deaminase and methionine gamma-lyase both contribute to isoleucine biosynthesis in plants. Therefore, isoleucine content can be altered by manipulating the expression of either or both of these enzymes. Additionally, both enzymes contribute to the up to 100-fold increase in isoleucine that is observed in drought-stressed Arabidopsis. Toward the end of the project it was discovered that through different projects, both groups had been able to independently up-regulate phenylalanine accumulation by different mechanisms. The Galili lab transformed Arabidopsis with a feedbackinsensitive bacterial enzyme and the Jander lab found a feedback insensitive mutation in Arabidopsis arogenate dehydratase. Exchange of the respective plant lines has allowed a comparative analysis of the different methods for increasing phenylalanine content and the creation of double mutants. The research that was conducted as part of this BARD project has led to new insights into plant amino acid metabolism. Additionally, new approaches that were found to increase the accumulation of threonine, isoleucine, and phenylalanine in plants have potential practical applications. Increased threonine and isoleucine levels can increase the nutritional value of crop plants. Elevated isoleucine accumulation may increase the osmotic stress tolerance of plants. Up-regulation of phenylalanine biosynthesis can be used to increase the production of downstream higher-value plant metabolites of biofuel feed stocks.
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