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  1. Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coff...

    Authors: Romain Guyot, Florent Lefebvre-Pautigny, Christine Tranchant-Dubreuil, Michel Rigoreau, Perla Hamon, Thierry Leroy, Serge Hamon, Valérie Poncet, Dominique Crouzillat and Alexandre de Kochko
    Citation: BMC Genomics 2012 13:103
    Content type: Research article Published on:

  2. Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport...

    Authors: Anita Zamboni, Laura Zanin, Nicola Tomasi, Mario Pezzotti, Roberto Pinton, Zeno Varanini and Stefano Cesco
    Citation: BMC Genomics 2012 13:101
    Content type: Research article Published on:

  3. Sugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar. Sugar yield is compromised by reproductive growth hence crops must remain vegetative until harvest. Prolonged exposure to cold t...

    Authors: Effie S Mutasa-Göttgens, Anagha Joshi, Helen F Holmes, Peter Hedden and Berthold Göttgens
    Citation: BMC Genomics 2012 13:99
    Content type: Research article Published on:

  4. Marmosets are playing an increasingly large and important role in biomedical research. They share genetic, anatomical, and physiological similarities with humans and other primate model species, but their smal...

    Authors: Carolyn G Sweeney, Elizabeth Curran, Susan V Westmoreland, Keith G Mansfield and Eric J Vallender
    Citation: BMC Genomics 2012 13:98
    Content type: Research article Published on:

  5. In Drosophila melanogaster, the dosage-compensation system that equalizes X-linked gene expression between males and females, thereby assuring that an appropriate balance is maintained between the expression of g...

    Authors: Philge Philip, Fredrik Pettersson and Per Stenberg
    Citation: BMC Genomics 2012 13:97
    Content type: Research article Published on:

  6. Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication...

    Authors: Jin-Tu Wang, Jiong-Tang Li, Xiao-Feng Zhang and Xiao-Wen Sun
    Citation: BMC Genomics 2012 13:96
    Content type: Research article Published on:

  7. High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging...

    Authors: Yoshinari Moriguchi, Tokuko Ujino-Ihara, Kentaro Uchiyama, Norihiro Futamura, Maki Saito, Saneyoshi Ueno, Asako Matsumoto, Naoki Tani, Hideaki Taira, Kenji Shinohara and Yoshihiko Tsumura
    Citation: BMC Genomics 2012 13:95
    Content type: Research article Published on:

  8. Genome-wide gene expression profiling and detailed physiological investigation were used for understanding the molecular mechanism and physiological response of Gossypium herbaceum, which governs the adaptability...

    Authors: Alok Ranjan, Deepti Nigam, Mehar H Asif, Ruchi Singh, Sanjay Ranjan, Shrikant Mantri, Neha Pandey, Ila Trivedi, Krishan Mohan Rai, Satya N Jena, Bhupendra Koul, Rakesh Tuli, Uday V Pathre and Samir V Sawant
    Citation: BMC Genomics 2012 13:94
    Content type: Research article Published on:

  9. In rodent models and in humans the impact of gestational diets on the offspring's phenotype was shown experimentally and epidemiologically. Adverse environmental conditions during fetal development provoke an ...

    Authors: Michael Oster, Eduard Murani, Cornelia C Metges, Siriluck Ponsuksili and Klaus Wimmers
    Citation: BMC Genomics 2012 13:93
    Content type: Research article Published on:

  10. Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the c...

    Authors: Nicole Gruenheit, Oliver Deusch, Christian Esser, Matthias Becker, Claudia Voelckel and Peter Lockhart
    Citation: BMC Genomics 2012 13:92
    Content type: Research article Published on:

  11. A central goal in Huntington's disease (HD) research is to identify and prioritize candidate targets for neuroprotective intervention, which requires genome-scale information on the modifiers of early-stage ne...

    Authors: François-Xavier Lejeune, Lilia Mesrob, Frédéric Parmentier, Cedric Bicep, Rafael P Vazquez-Manrique, J Alex Parker, Jean-Philippe Vert, Cendrine Tourette and Christian Neri
    Citation: BMC Genomics 2012 13:91
    Content type: Research article Published on:

  12. The peanut (Arachis hypogaea L.) is an important oilseed crop in tropical and subtropical regions of the world. However, little about the molecular biology of the peanut is currently known. Recently, next-generat...

    Authors: Jianan Zhang, Shan Liang, Jialei Duan, Jin Wang, Silong Chen, Zengshu Cheng, Qiang Zhang, Xuanqiang Liang and Yurong Li
    Citation: BMC Genomics 2012 13:90
    Content type: Research article Published on:

  13. The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K...

    Authors: John P Bannantine, Chia-wei Wu, Chungyi Hsu, Shiguo Zhou, David C Schwartz, Darrell O Bayles, Michael L Paustian, David P Alt, Srinand Sreevatsan, Vivek Kapur and Adel M Talaat
    Citation: BMC Genomics 2012 13:89
    Content type: Research article Published on:

  14. Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant gen...

    Authors: Pimlapas Leekitcharoenphon, Oksana Lukjancenko, Carsten Friis, Frank M Aarestrup and David W Ussery
    Citation: BMC Genomics 2012 13:88
    Content type: Research article Published on:

  15. The Tasmanian devil (Sarcophilus harrisii) is currently under threat of extinction due to an unusual fatal contagious cancer called Devil Facial Tumour Disease (DFTD). DFTD is caused by a clonal tumour cell line ...

    Authors: Yuanyuan Cheng, Andrew Stuart, Katrina Morris, Robyn Taylor, Hannah Siddle, Janine Deakin, Menna Jones, Chris T Amemiya and Katherine Belov
    Citation: BMC Genomics 2012 13:87
    Content type: Research article Published on:

  18. Small intestine and liver greatly contribute to whole body lipid, cholesterol and phospholipid metabolism but to which extent cholesterol and phospholipid handling in these tissues is affected by high fat West...

    Authors: Charles Desmarchelier, Christoph Dahlhoff, Sylvia Keller, Manuela Sailer, Gerhard Jahreis and Hannelore Daniel
    Citation: BMC Genomics 2012 13:84
    Content type: Research article Published on:

  19. MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have bee...

    Authors: Pablo Peláez, Minerva S Trejo, Luis P Iñiguez, Georgina Estrada-Navarrete, Alejandra A Covarrubias, José L Reyes and Federico Sanchez
    Citation: BMC Genomics 2012 13:83
    Content type: Research article Published on:

  20. The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The foc...

    Authors: Neil R Hackett, Marcus W Butler, Renat Shaykhiev, Jacqueline Salit, Larsson Omberg, Juan L Rodriguez-Flores, Jason G Mezey, Yael Strulovici-Barel, Guoqing Wang, Lukas Didon and Ronald G Crystal
    Citation: BMC Genomics 2012 13:82
    Content type: Research article Published on:

  21. There has been an increasing body of epidemiologic and biochemical evidence implying the role of cerebral insulin resistance in Alzheimer-type dementia. For a better understanding of the insulin effect on the ...

    Authors: Omar Abdul-Rahman, Maria Sasvari-Szekely, Agota Ver, Klara Rosta, Bernadett K Szasz, Eva Kereszturi and Gergely Keszler
    Citation: BMC Genomics 2012 13:81
    Content type: Research article Published on:

  22. Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop,...

    Authors: Cristina Esteras, Pedro Gómez, Antonio J Monforte, José Blanca, Nelly Vicente-Dólera, Cristina Roig, Fernando Nuez and Belén Picó
    Citation: BMC Genomics 2012 13:80
    Content type: Research article Published on:

  23. The importance of peptide microarrays as a tool for serological diagnostics has strongly increased over the last decade. However, interpretation of the binding signals is still hampered by our limited understa...

    Authors: Victor Greiff, Henning Redestig, Juliane Lück, Nicole Bruni, Atijeh Valai, Susanne Hartmann, Sebastian Rausch, Johannes Schuchhardt and Michal Or-Guil
    Citation: BMC Genomics 2012 13:79
    Content type: Research article Published on:

  24. The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this ...

    Authors: Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charles D Johnson and Scott V Dindot
    Citation: BMC Genomics 2012 13:78
    Content type: Research article Published on:

  25. Restriction Enzyme-based Reduced Representation Library (RRL) method represents a relatively feasible and flexible strategy used for Single Nucleotide Polymorphism (SNP) identification in different species. It...

    Authors: Ye Du, Hui Jiang, Ying Chen, Cong Li, Meiru Zhao, Jinghua Wu, Yong Qiu, Qibin Li and Xiuqing Zhang
    Citation: BMC Genomics 2012 13:77
    Content type: Research article Published on:

  26. Although sexual reproduction is dominant within eukaryotes, asexual reproduction is widespread and has evolved independently as a derived trait in almost all major taxa. How asexuality evolved in sexual organi...

    Authors: Aurore Gallot, Shuji Shigenobu, Tomomi Hashiyama, Stéphanie Jaubert-Possamai and Denis Tagu
    Citation: BMC Genomics 2012 13:76
    Content type: Research article Published on:

  27. The potato genome sequence derived from the Solanum tuberosum Group Phureja clone DM1-3 516 R44 provides unparalleled insight into the genome composition and organisation of this important crop. A key class of ge...

    Authors: Florian Jupe, Leighton Pritchard, Graham J Etherington, Katrin MacKenzie, Peter JA Cock, Frank Wright, Sanjeev Kumar Sharma, Dan Bolser, Glenn J Bryan, Jonathan DG Jones and Ingo Hein
    Citation: BMC Genomics 2012 13:75
    Content type: Research article Published on:

  29. The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities betwe...

    Authors: Joseph A Christie-Oleza, Guylaine Miotello and Jean Armengaud
    Citation: BMC Genomics 2012 13:73
    Content type: Research article Published on:

  30. The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substant...

    Authors: Jennifer Monson-Miller, Diana C Sanchez-Mendez, Joseph Fass, Isabelle M Henry, Thomas H Tai and Luca Comai
    Citation: BMC Genomics 2012 13:72
    Content type: Methodology article Published on:

  31. An array of experimental models have been developed in the small model organisms C. elegans, S. cerevisiae and D. melanogaster for the study of various neurodegenerative diseases including Alzheimer's disease, Pa...

    Authors: Xi Chen and Robert D Burgoyne
    Citation: BMC Genomics 2012 13:71
    Content type: Research article Published on:

  32. The evolution of sociality in spiders involves a transition from an outcrossing to a highly inbreeding mating system, a shift to a female biased sex ratio, and an increase in the reproductive skew among indivi...

    Authors: Tiina M Mattila, Jesper S Bechsgaard, Troels T Hansen, Mikkel H Schierup and Trine Bilde
    Citation: BMC Genomics 2012 13:70
    Content type: Research article Published on:

  33. Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymme...

    Authors: Stefan Engelen, David Vallenet, Claudine Médigue and Antoine Danchin
    Citation: BMC Genomics 2012 13:69
    Content type: Research article Published on:

  34. Haemophilus parasuis (H. parasuis) is the etiological agent of Glässer's disease in pigs. Currently, the molecular basis of this infection is largely unknown. The innate immune response is the first line of defen...

    Authors: Yang Wang, Chong Liu, Ying Fang, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen and Qigai He
    Citation: BMC Genomics 2012 13:68
    Content type: Research article Published on:

  35. Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0), aluminum (Al) remains in a cationic form that is toxic to plants, r...

    Authors: Agnieszka Niedziela, Piotr T Bednarek, Henryk Cichy, Grzegorz Budzianowski, Andrzej Kilian and Andrzej Anioł
    Citation: BMC Genomics 2012 13:67
    Content type: Research article Published on:

  36. We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in informatio...

    Authors: Jon Bohlin, Mark WJ van Passel, Lars Snipen, Anja B Kristoffersen, David Ussery and Simon P Hardy
    Citation: BMC Genomics 2012 13:66
    Content type: Research article Published on:

  38. Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is ...

    Authors: Dong An, Jun Yang and Peng Zhang
    Citation: BMC Genomics 2012 13:64
    Content type: Research article Published on:

  39. Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and ...

    Authors: Jennifer S Tolman and Miguel A Valvano
    Citation: BMC Genomics 2012 13:63
    Content type: Research article Published on:

  40. Aspergillus fumigatus is a mold responsible for the majority of cases of aspergillosis in humans. To survive in the human body, A. fumigatus must adapt to microenvironments that are often characterized by low nut...

    Authors: Bridget M Barker, Kristin Kroll, Martin Vödisch, Aurélien Mazurie, Olaf Kniemeyer and Robert A Cramer
    Citation: BMC Genomics 2012 13:62
    Content type: Research article Published on:

  42. Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essent...

    Authors: Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su and Tao Wang
    Citation: BMC Genomics 2012 13:60
    Content type: Database Published on:

  43. Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, s...

    Authors: Daniel Nätt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson and Per Jensen
    Citation: BMC Genomics 2012 13:59
    Content type: Research article Published on:

  45. Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemi)cellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant infor...

    Authors: Marie Couturier, David Navarro, Caroline Olivé, Didier Chevret, Mireille Haon, Anne Favel, Laurence Lesage-Meessen, Bernard Henrissat, Pedro M Coutinho and Jean-Guy Berrin
    Citation: BMC Genomics 2012 13:57
    Content type: Research article Published on:

  46. Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known prokaryotes capable of oxygenic photosyn...

    Authors: Christian Beck, Henning Knoop, Ilka M Axmann and Ralf Steuer
    Citation: BMC Genomics 2012 13:56
    Content type: Research article Published on:

  47. Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gen...

    Authors: Fekadu Yadetie, Stephen Butcher, Hilde E Førde, Coen Campsteijn, Jean-Marie Bouquet, Odd A Karlsen, France Denoeud, Raghu Metpally, Eric M Thompson, J Robert Manak, Anders Goksøyr and Daniel Chourrout
    Citation: BMC Genomics 2012 13:55
    Content type: Research article Published on:

  48. Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological spe...

    Authors: Yolanda Guillén and Alfredo Ruiz
    Citation: BMC Genomics 2012 13:53
    Content type: Research article Published on:

  49. Many biological systems respond to the presence or absence of gravity. Since experiments performed in space are expensive and can only be undertaken infrequently, Earth-based simulation techniques are used to ...

    Authors: Raul Herranz, Oliver J Larkin, Camelia E Dijkstra, Richard JA Hill, Paul Anthony, Michael R Davey, Laurence Eaves, Jack JWA van Loon, F Javier Medina and Roberto Marco
    Citation: BMC Genomics 2012 13:52
    Content type: Research article Published on:

  50. In a previous genome-wide analysis of FXR binding to hepatic chromatin, we noticed that an extra nuclear receptor (NR) half-site was co-enriched close to the FXR binding IR-1 elements and we provided limited s...

    Authors: Hansook Kim Chong, Jacob Biesinger, Young-Kyo Seo, Xiaohui Xie and Timothy F Osborne
    Citation: BMC Genomics 2012 13:51
    Content type: Research article Published on:

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BMC Genomics

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