DNA from dust: comparative genomics of large DNA viruses in field surveillance samples
Utsav PandeyAndrew S. BellDaniel W. RennerDavid KennedyJacob ShreveChris L. CairnsMatthew J. JonesPatricia A. DunnAndrew F. ReadMoriah L. Szpara
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Abstract The intensification of the poultry industry over the last sixty years facilitated the evolution of increased virulence and vaccine breaks in Marek’s disease virus (MDV-1). Full genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing. We applied this to the first characterization of MDV-1 genomes from the field, without prior culture. These viruses were collected from vaccinated hosts that acquired naturally circulating field strains of MDV-1, in the absence of a disease outbreak. This reflects the current issue afflicting the poultry industry, where virulent field strains continue to circulate despite vaccination, and can remain undetected due to the lack of overt disease symptoms. We found that viral genomes from adjacent field sites had high levels of overall DNA identity, and despite strong evidence of purifying selection, had coding variations in proteins associated with virulence and manipulation of host immunity. Our methods empower ecological field surveillance, make it possible to determine the basis of viral virulence and vaccine breaks, and can be used to obtain full genomes from clinical samples of other large DNA viruses, known and unknown.Keywords:
Comparative Genomics
A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.
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Horizontal Gene Transfer
Bacterial genome size
Functional Genomics
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Comparative Genomics
Synteny
Functional Genomics
Identification
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Comparative Genomics
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As a type of ancient eukaryote,Giardia lamblia has played a very important role in the process of biological evolution.Comparative genomics can reveal the evolutionary relationships of G.lambliaat the genetic level and further clarify the role of G.lambliain the process of biological evolution.This review describes the main research techniques used in comparative genomics and it describes the use of comparative genomics to study the biological evolution of G.lamblia.This review also discusses the prospects for using comparative genomics to study G.lamblia.
Comparative Genomics
Giardia lamblia
Eukaryote
Convergent evolution
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Abstract Comparative genomics involves the comparison of features of completely sequenced (or nearly so) genomes. Comparative sequence analyses facilitate both the functional annotation of genomes and whole‐genome approaches to evolutionary issues. We present a review of the field of comparative genomics and point out how the comparative approach can be used to help better understand the human genome sequence.
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Sequence (biology)
Personal genomics
Functional Genomics
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Comparative genomics is a science in its infancy. It has been driven by a huge increase in freely available genome-sequence data, and the development of computer techniques to allow whole-genome sequence analyses. Other approaches, which use hybridization as a method for comparing the gene content of related organisms, are rising alongside these more bioinformatic methods. All these approaches have been pioneered using bacterial genomes because of their simplicity and the large number of complete genome sequences available. The aim of bacterial comparative genomics is to determine what genotypic differences are important for the expression of particular traits (e.g., antibiotic resistance, virulence, or host preference). The benefits of such studies will be a deeper understanding of these phenomena; the possibility of exposing novel drug targets, including those for antivirulence drugs; and the development of molecular techniques that reveal patients who are infected with virulent organisms so that health care resources can be allocated appropriately. With more and more genome sequences becoming available, the rise of comparative genomics continues apace.
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Functional Genomics
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1. Merhej V, Georgiades K, Raoult D. Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors. Brief Funct Genomics 2013;12:291–304. 2. Chua KY, Stinear TP, Howden BP. Functional genomics of Staphylococcusaureus. BriefFunctGenomics 2013; 12:305–15. 3. Tymoshenko S, Oppenheim RD, Soldati-Favre D, et al. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics 2013;12:316–27. 4. Del Tordello E, Serruto D. Functional genomics studies of the human pathogen Neisseria meningitidis. Brief Funct Genomics 2013;12:328–40. 5. de Barsy M, Greub G. Functional genomics of intracellular bacteria. Brief FunctGenomics 2013;12:341–53.
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Placing genomes into an evolutionary framework has proved to be usefol for deciphering the genome sequences of organisms.Comparative genomies,as a routine toolkit.has substantially incteased the understanding of the processes by which bacterial genomes evolve and led to a re-evaluation of the history of life.In this review,we present some of the most important recent advances and promising leads in the field of bacterial evolutionary genomics.
Key words:
Comparative genomics; HGT; Phylogeny
Comparative Genomics
Bacterial genome size
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Wheat is the heterogenous polyploid plant with large chromosomes and high level of repetitive sequences. These characters have limited the progress of wheat genomics studies. Comparative genomics provided a platform for study of wheat genomics by using model plants Functional genomics focused on the expressed portion of the wheat genome. Its aim was determining the expression and function of genes. This paper reviews the application of comparative genomics in wheat genomic studies and the contents and methods of functional genomics of wheat.
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Comparative Genomics
Polyploid
Structural genomics
Genome Biology
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Synteny
Comparative Genomics
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