Structural flexibility in the Burkholderia mallei genome
William C. NiermanDavid DeShazerSun KimHervé TettelinWilliam NelsonTamara V. FeldblyumRicky L. UlrichCatherine M. RonningLauren BrinkacSean C. DaughertyTanja DavidsenRobert T. DeBoyGeorge DimitrovRobert J. DodsonA. Scott DurkinMichelle GwinnDaniel H. HaftHoda KhouriJames F. KolonayRamana MadupuYasmin MohammoudWilliam NelsonDiana RaduneClaudia Mabel Terenti RomeroSaul SarriaJeremy SelengutChristine ShamblinSteven A. SullivanOwen WhiteYan YuNikhat ZafarLi‐Wei ZhouClaire M. Fraser
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Abstract:
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei , the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo . The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei . The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection.Keywords:
Comparative Genomics
Antigenic variation
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
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Population 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
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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.
Comparative Genomics
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.
Comparative Genomics
Functional Genomics
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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.
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Comparative genomics; HGT; Phylogeny
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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 is one of the important research fields in genomics. By comparative genomic studies it was possible to establish a giant genetic system beyond one species which might be significant to tree. Comparative genomics in Salicaceae, Pinaceae, Rosaceae, Fagaceae and Hamamelidaceae had shown that the organization of genomes remained highly conserved over long evolutionary periods and extensive synteny or collinarity or microcollinarity existed in tree genomes. A total of 13,019 pairs of orthologs were identified between genes in Populus and Arabidopsis using the best bidirectional Basic Local Alignment Search Tool (BLAST) hits, with an average mutual coverage of these alignments equal to 93%; 11,654 pairs of orthologs had greater than 90% alignment of gene lengths. The progress of comparative genomics in tree species was reviewed and the prospect of this field was discussed, which might be useful to tree genomics in China.
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Synteny
Functional Genomics
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