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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 18 of 19

  1. Meiotic recombination events are not randomly located, but rather cluster at hotspot regions. Recently, the fine-scale mapping of genome-wide human recombination hotspots was performed. Here, we systematically...

    Authors: Tao Zhou, Zhibin Hu, Zuomin Zhou, Xuejiang Guo and Jiahao Sha

    Citation: BMC Genomics 2013 14:67

    Content type: Research article

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  2. Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of su...

    Authors: Carsten Kuenne, André Billion, Mobarak Abu Mraheil, Axel Strittmatter, Rolf Daniel, Alexander Goesmann, Sukhadeo Barbuddhe, Torsten Hain and Trinad Chakraborty

    Citation: BMC Genomics 2013 14:47

    Content type: Research article

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  3. The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also u...

    Authors: Ryo Kakioka, Tomoyuki Kokita, Hiroki Kumada, Katsutoshi Watanabe and Noboru Okuda

    Citation: BMC Genomics 2013 14:32

    Content type: Research article

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  4. The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic...

    Authors: Wen-Sui Lo, Ling-Ling Chen, Wan-Chia Chung, Gail E Gasparich and Chih-Horng Kuo

    Citation: BMC Genomics 2013 14:22

    Content type: Research article

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  5. Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny ...

    Authors: Hugo J Parker, Paul Piccinelli, Tatjana Sauka-Spengler, Marianne Bronner and Greg Elgar

    Citation: BMC Genomics 2011 12:637

    Content type: Research article

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  6. Driven essentially by random genetic drift, subfunctionalization has been identified as a possible non-adaptive mechanism for the retention of duplicate genes in small-population species, where widespread dele...

    Authors: Ariel Fernández, Yun-Huei Tzeng and Sze-Bi Hsu

    Citation: BMC Genomics 2011 12:604

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2013 14:260

  7. Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when nat...

    Authors: Frédéric JJ Chain, Jonathan Dushoff and Ben J Evans

    Citation: BMC Genomics 2011 12:599

    Content type: Research article

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  8. The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most sp...

    Authors: Maximilian P Nesnidal, Martin Helmkampf, Iris Bruchhaus and Bernhard Hausdorf

    Citation: BMC Genomics 2011 12:572

    Content type: Research article

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  9. Mammalian olfactory receptors (ORs) are subject to a remarkable but poorly understood regime of transcriptional regulation, whereby individual olfactory neurons each express only one allele of a single member ...

    Authors: Janet M Young, Ralf M Luche and Barbara J Trask

    Citation: BMC Genomics 2011 12:561

    Content type: Research article

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  10. Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to dif...

    Authors: Gregory Gimenez, Claire Bertelli, Claire Moliner, Catherine Robert, Didier Raoult, Pierre-Edouard Fournier and Gilbert Greub

    Citation: BMC Genomics 2011 12:542

    Content type: Research article

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  11. Changes in transcriptional regulation underlie many of the phenotypic differences observed within and between species of bacteria. Lateral genetic transfer (LGT) can significantly impact the transcription fact...

    Authors: Elizabeth Skippington and Mark A Ragan

    Citation: BMC Genomics 2011 12:532

    Content type: Research article

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  12. The study of gene families is pivotal for the understanding of gene evolution across different organisms and such phylogenetic background is often used to infer biochemical functions of genes. Modern high-thro...

    Authors: Thomas Meinel, Michal R Schweiger, Andreas H Ludewig, Ramu Chenna, Sylvia Krobitsch and Ralf Herwig

    Citation: BMC Genomics 2011 12:483

    Content type: Software

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  13. Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity.

    Authors: Xiyin Wang, Manuel J Torres, Gary Pierce, Cornelia Lemke, Lisa K Nelson, Bayram Yuksel, John E Bowers, Barry Marler, Yongli Xiao, Lifeng Lin, Ethan Epps, Heidi Sarazen, Carl Rogers, Santhosh Karunakaran, Jennifer Ingles, Emily Giattina…

    Citation: BMC Genomics 2011 12:470

    Content type: Research article

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  14. A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identica...

    Authors: Daniel P Howrigan, Matthew A Simonson and Matthew C Keller

    Citation: BMC Genomics 2011 12:460

    Content type: Methodology article

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  15. Invasive species are valuable model systems for examining the evolutionary processes and molecular mechanisms associated with their specific characteristics by comparison with closely related species. Over the...

    Authors: Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yun-Lin Su, Jun Xia and Shu-Sheng Liu

    Citation: BMC Genomics 2011 12:458

    Content type: Research article

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  16. The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed the...

    Authors: Timothy R Schmidt, Edgar J Scott II and David W Dyer

    Citation: BMC Genomics 2011 12:430

    Content type: Research article

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  17. Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human gen...

    Authors: Kazuharu Misawa

    Citation: BMC Genomics 2011 12:397

    Content type: Research article

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  18. The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that ...

    Authors: Stephen L Cameron, Kazunori Yoshizawa, Atsushi Mizukoshi, Michael F Whiting and Kevin P Johnson

    Citation: BMC Genomics 2011 12:394

    Content type: Research article

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  19. Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and ...

    Authors: Christof Francke, Tom Groot Kormelink, Yanick Hagemeijer, Lex Overmars, Vincent Sluijter, Roy Moezelaar and Roland J Siezen

    Citation: BMC Genomics 2011 12:385

    Content type: Research article

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  20. Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequenc...

    Authors: Zhengdong D Zhang, Jiang Du, Hugo Lam, Alex Abyzov, Alexander E Urban, Michael Snyder and Mark Gerstein

    Citation: BMC Genomics 2011 12:375

    Content type: Methodology article

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  21. Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been s...

    Authors: Xiaobin Zheng, Gang-Qing Hu, Zhen-Su She and Huaiqiu Zhu

    Citation: BMC Genomics 2011 12:361

    Content type: Research article

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  22. The cell suicide pathway of apoptosis is a necessary event in the life of multicellular organisms. It is involved in many biological processes ranging from development to the immune response. Evolutionarily co...

    Authors: Juliette Courtiade, Yannick Pauchet, Heiko Vogel and David G Heckel

    Citation: BMC Genomics 2011 12:357

    Content type: Research article

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  23. MicroRNAs (miRNAs) are non-coding RNAs with important roles in regulating gene expression. Recent studies indicate that transcription and cleavage of miRNA are coupled, and that chromatin structure may influen...

    Authors: Shijia Zhu, Qinghua Jiang, Guohua Wang, Bo Liu, Mingxiang Teng and Yadong Wang

    Citation: BMC Genomics 2011 12:329

    Content type: Research article

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  24. The regulatory information encoded in the DNA of promoter regions usually enforces a minimal, non-zero distance between the coding regions of neighboring genes. However, the size of this minimal regulatory spa...

    Authors: Wei-Hua Chen, Wu Wei and Martin J Lercher

    Citation: BMC Genomics 2011 12:320

    Content type: Research article

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  25. Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmoni...

    Authors: Carine Genet, Patrice Dehais, Yniv Palti, Guangtu Gao, Frederick Gavory, Patrick Wincker, Edwige Quillet and Mekki Boussaha

    Citation: BMC Genomics 2011 12:314

    Content type: Research article

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  26. Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years t...

    Authors: Daniel M Tiago, Vincent Laizé, Luca Bargelloni, Serena Ferraresso, Chiara Romualdi and M Leonor Cancela

    Citation: BMC Genomics 2011 12:310

    Content type: Research article

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  27. Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements als...

    Authors: Amélie S Véron, Claire Lemaitre, Christian Gautier, Vincent Lacroix and Marie-France Sagot

    Citation: BMC Genomics 2011 12:303

    Content type: Research article

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  28. Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is ...

    Authors: Paul J McMurdie, Laura A Hug, Elizabeth A Edwards, Susan Holmes and Alfred M Spormann

    Citation: BMC Genomics 2011 12:287

    Content type: Research article

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  29. Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of...

    Authors: Brian B Oakley, Eldin Talundzic, Cesar A Morales, Kelli L Hiett, Gregory R Siragusa, Nikolay V Volozhantsev and Bruce S Seal

    Citation: BMC Genomics 2011 12:282

    Content type: Research article

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  30. The total number of miRNA genes in a genome, expression of which is responsible for the miRNA repertoire of an organism, is not precisely known. Moreover, the question of how new miRNA genes arise during evolu...

    Authors: Stefan Lehnert, Vladimir Kapitonov, Pushpike J Thilakarathne and Frans C Schuit

    Citation: BMC Genomics 2011 12:257

    Content type: Research article

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  31. The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancesto...

    Authors: Bo Zhu, Miao-Miao Lou, Guan-Lin Xie, Guo-Qing Zhang, Xue-Ping Zhou, Bin Li and Gu-Lei Jin

    Citation: BMC Genomics 2011 12:248

    Content type: Research article

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  32. Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR en...

    Authors: Alessandra F Ribas, Alberto Cenci, Marie-Christine Combes, Hervé Etienne and Philippe Lashermes

    Citation: BMC Genomics 2011 12:240

    Content type: Research article

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  33. BAHD acyltransferases are involved in the synthesis and elaboration of a wide variety of secondary metabolites. Previous research has shown that characterized proteins from this family fall broadly into five m...

    Authors: Lindsey K Tuominen, Virgil E Johnson and Chung-Jui Tsai

    Citation: BMC Genomics 2011 12:236

    Content type: Research article

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  34. The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitoc...

    Authors: Enrico Negrisolo, Massimiliano Babbucci and Tomaso Patarnello

    Citation: BMC Genomics 2011 12:221

    Content type: Research article

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  35. Schistosomiasis remains an important parasitic disease and a major economic problem in many countries. The Schistosoma mansoni genome and predicted proteome sequences were recently published providing the opportu...

    Authors: Luiza F Andrade, Laila A Nahum, Lívia GA Avelar, Larissa L Silva, Adhemar Zerlotini, Jerônimo C Ruiz and Guilherme Oliveira

    Citation: BMC Genomics 2011 12:215

    Content type: Research article

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  36. Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the ...

    Authors: Robert Boissy, Azad Ahmed, Benjamin Janto, Josh Earl, Barry G Hall, Justin S Hogg, Gordon D Pusch, Luisa N Hiller, Evan Powell, Jay Hayes, Susan Yu, Sandeep Kathju, Paul Stoodley, J Christopher Post, Garth D Ehrlich and Fen Z Hu

    Citation: BMC Genomics 2011 12:187

    Content type: Research article

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  37. Alu elements are the most abundant retrotransposable elements comprising ~11% of the human genome. Many studies have highlighted the role that Alu elements have in genetic instability and how their contribution t...

    Authors: Wensheng Zhang, Andrea Edwards, Wei Fan, Prescott Deininger and Kun Zhang

    Citation: BMC Genomics 2011 12:157

    Content type: Research article

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  38. Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomi...

    Authors: Robert HS Kraus, Hindrik HD Kerstens, Pim Van Hooft, Richard PMA Crooijmans, Jan J Van Der Poel, Johan Elmberg, Alain Vignal, Yinhua Huang, Ning Li, Herbert HT Prins and Martien AM Groenen

    Citation: BMC Genomics 2011 12:150

    Content type: Research article

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  39. Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular ch...

    Authors: Neha Potnis, Ksenia Krasileva, Virginia Chow, Nalvo F Almeida, Prabhu B Patil, Robert P Ryan, Molly Sharlach, Franklin Behlau, J Max Dow, MT Momol, Frank F White, James F Preston, Boris A Vinatzer, Ralf Koebnik, João C Setubal, David J Norman…

    Citation: BMC Genomics 2011 12:146

    Content type: Research article

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  40. Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, th...

    Authors: Zhixi Tian, Yanjun Yu, Feng Lin, Yeisoo Yu, Phillip J SanMiguel, Rod A Wing, Susan R McCouch, Jianxin Ma and Scott A Jackson

    Citation: BMC Genomics 2011 12:142

    Content type: Research article

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  41. The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagio...

    Authors: Francois Thiaucourt, Lucia Manso-Silvan, Woubit Salah, Valérie Barbe, Benoit Vacherie, Daniel Jacob, Marc Breton, Virginie Dupuy, Anne Marie Lomenech, Alain Blanchard and Pascal Sirand-Pugnet

    Citation: BMC Genomics 2011 12:114

    Content type: Research article

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