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  1. Nodulation and symbiotic nitrogen fixation are mediated by several genes, both of the host legume and of the bacterium. The rhizobial regulatory nodD gene plays a critical role, orchestrating the transcription of...

    Authors: Pablo del Cerro, Amanda Alves Paiva Rolla-Santos, Douglas Fabiano Gomes, Bettina Berquó Marks, Francisco Pérez-Montaño, Miguel Ángel Rodríguez-Carvajal, André Shigueyoshi Nakatani, Antonio Gil-Serrano, Manuel Megías, Francisco Javier Ollero and Mariangela Hungria
    Citation: BMC Genomics 2015 16:251
    Content type: Research article Published on:

  2. Several studies have revealed a potential role for both small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) in the physiopathology of relapsing-remitting multiple sclerosis (RRMS). This potential implication...

    Authors: Haritz Irizar, Maider Muñoz-Culla, Matías Sáenz-Cuesta, Iñaki Osorio-Querejeta, Lucía Sepúlveda, Tamara Castillo-Triviño, Alvaro Prada, Adolfo Lopez de Munain, Javier Olascoaga and David Otaegui
    Citation: BMC Genomics 2015 16:250
    Content type: Research article Published on:

  3. Chimeric read-through RNAs are transcripts originating from two directly adjacent genes (<10 kb) on the same DNA strand. Although they are found in next-generation whole transcriptome sequencing (RNA-Seq) data...

    Authors: Dorothee Pflueger, Christiane Mittmann, Silvia Dehler, Mark A Rubin, Holger Moch and Peter Schraml
    Citation: BMC Genomics 2015 16:247
    Content type: Research article Published on:

  4. Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Am...

    Authors: A Paola Zuluaga, Montserrat Solé, Haibin Lu, Elsa Góngora-Castillo, Brieanne Vaillancourt, Nuria Coll, C Robin Buell and Marc Valls
    Citation: BMC Genomics 2015 16:246
    Content type: Research article Published on:

  5. Cold storage induces chilling injury (CI) disorders in peach fruit (woolliness/mealiness, flesh browning and reddening/bleeding) manifested when ripened at shelf life. To gain insight into the mechanisms under...

    Authors: Clara Pons Puig, Anurag Dagar, Cristina Marti Ibanez, Vikram Singh, Carlos H Crisosto, Haya Friedman, Susan Lurie and Antonio Granell
    Citation: BMC Genomics 2015 16:245
    Content type: Research article Published on:

  7. With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of...

    Authors: Lindsay L Traeger, Jeremy D Volkening, Howell Moffett, Jason R Gallant, Po-Hao Chen, Carl D Novina, George N Phillips Jr, Rene Anand, Gregg B Wells, Matthew Pinch, Robert Güth, Graciela A Unguez, James S Albert, Harold Zakon, Michael R Sussman and Manoj P Samanta
    Citation: BMC Genomics 2015 16:243
    Content type: Research article Published on:

  8. Efficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock ...

    Authors: Polyana C Tizioto, Luiz L Coutinho, Jared E Decker, Robert D Schnabel, Kamila O Rosa, Priscila SN Oliveira, Marcela M Souza, Gerson B Mourão, Rymer R Tullio, Amália S Chaves, Dante PD Lanna, Adhemar Zerlotini-Neto, Mauricio A Mudadu, Jeremy F Taylor and Luciana CA Regitano
    Citation: BMC Genomics 2015 16:242
    Content type: Research article Published on:

  10. Lactobacillus hokkaidonensis is an obligate heterofermentative lactic acid bacterium, which is isolated from Timothy grass silage in Hokkaido, a subarctic region of Japan. This bacterium is exp...

    Authors: Yasuhiro Tanizawa, Masanori Tohno, Eli Kaminuma, Yasukazu Nakamura and Masanori Arita
    Citation: BMC Genomics 2015 16:240
    Content type: Research article Published on:

  11. Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species a...

    Authors: Ha X Dang, Barry Pryor, Tobin Peever and Christopher B Lawrence
    Citation: BMC Genomics 2015 16:239
    Content type: Database Published on:

  12. Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems app...

    Authors: Wai Yi Leung, Tobias Marschall, Yogesh Paudel, Laurent Falquet, Hailiang Mei, Alexander Schönhuth and Tiffanie Yael Maoz (Moss)
    Citation: BMC Genomics 2015 16:238
    Content type: Research article Published on:

  13. RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functio...

    Authors: Francisco E Nicolás, Ana Vila, Simon Moxon, María D Cascales, Santiago Torres-Martínez, Rosa M Ruiz-Vázquez and Victoriano Garre
    Citation: BMC Genomics 2015 16:237
    Content type: Research article Published on:

  14. The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging du...

    Authors: Rachid Ounit, Steve Wanamaker, Timothy J Close and Stefano Lonardi
    Citation: BMC Genomics 2015 16:236
    Content type: Research Article Published on:

  17. Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was ...

    Authors: Rahul Sharma, Sören Gassel, Sabine Steiger, Xiaojuan Xia, Robert Bauer, Gerhard Sandmann and Marco Thines
    Citation: BMC Genomics 2015 16:233
    Content type: Research article Published on:

  18. For heterozygous genes, alleles on the chromatin from two different parents exhibit histone modification variations known as allele-specific histone modifications (ASHMs). The regulation of allele-specific gen...

    Authors: Zhibin Guo, Gaoyuan Song, Zhenwei Liu, Xuefeng Qu, Rong Chen, Daiming Jiang, Yunfang Sun, Chuan Liu, Yingguo Zhu and Daichang Yang
    Citation: BMC Genomics 2015 16:232
    Content type: Research article Published on:

  19. L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gi...

    Authors: Jonatan C Campillo-Brocal, María Dolores Chacón-Verdú, Patricia Lucas-Elío and Antonio Sánchez-Amat
    Citation: BMC Genomics 2015 16:231
    Content type: Research article Published on:

  20. Castor oil is the only commercial source of hydroxy fatty acid that has industrial value. The production of castor oil is hampered by the presence of the toxin ricin in its seed. Lesquerella seed also accumula...

    Authors: Hyun Uk Kim and Grace Qianhong Chen
    Citation: BMC Genomics 2015 16:230
    Content type: Research article Published on:

  21. RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencin...

    Authors: Richard J Orton, Caroline F Wright, Marco J Morelli, David J King, David J Paton, Donald P King and Daniel T Haydon
    Citation: BMC Genomics 2015 16:229
    Content type: Research article Published on:

  22. Brachypodium distachyon is emerging as a widely recognized model plant that has very close relations with several economically important Poaceae species. MAPK cascade is known to be an evolutio...

    Authors: Min Jiang, Feng Wen, Jianmei Cao, Peng Li, Jessica She and Zhaoqing Chu
    Citation: BMC Genomics 2015 16:228
    Content type: Research article Published on:

  23. Plant basic leucine zipper (bZIP) transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes. Brachypodium distachyon is emerging as a wi...

    Authors: Xiang Liu and Zhaoqing Chu
    Citation: BMC Genomics 2015 16:227
    Content type: Research article Published on:

  24. The whitefly Bemisia tabaci is an important agricultural pest with global distribution. This phloem-sap feeder harbors a primary symbiont, “Candidatus Portiera aleyrodidarum”, which compensates for the deficient ...

    Authors: Qiong Rao, Pierre-Antoine Rollat-Farnier, Dan-Tong Zhu, Diego Santos-Garcia, Francisco J Silva, Andrés Moya, Amparo Latorre, Cecilia C Klein, Fabrice Vavre, Marie-France Sagot, Shu-Sheng Liu, Laurence Mouton and Xiao-Wei Wang
    Citation: BMC Genomics 2015 16:226
    Content type: Research article Published on:

  25. The fruit of litchi (Litchi chinensis) comprises a white translucent edible aril surrounded by a pericarp. The pericarp of litchi has been the focus of studies associated with fruit size, coloration, cracking and...

    Authors: Biao Lai, Bing Hu, Yong-Hua Qin, Jie-Tang Zhao, Hui-Cong Wang and Gui-Bing Hu
    Citation: BMC Genomics 2015 16:225
    Content type: Research article Published on:

  26. Jasmonic acid (JA) and methyl jasmonate (MeJA) regulate plant development, resistance to stress, and insect attack by inducing specific gene expression. However, little is known about the mechanism of plant de...

    Authors: Yi Tong Zhang, Yu Liang Zhang, Si Xue Chen, Guo Hua Yin, Ze Zhong Yang, Samantha Lee, Chun Guang Liu, Dan Dan Zhao, Yu Kun Ma, Fu Qiang Song, Joan W Bennett and Feng Shan Yang
    Citation: BMC Genomics 2015 16:224
    Content type: Research article Published on:

  27. Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domesticat...

    Authors: Chen Jiao, Min Gao, Xiping Wang and Zhangjun Fei
    Citation: BMC Genomics 2015 16:223
    Content type: Research article Published on:

  28. Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have...

    Authors: Rasmus Liedigk, Jakob Kolleck, Kai O Böker, Erik Meijaard, Badrul Munir Md-Zain, Muhammad Abu Bakar Abdul-Latiff, Ahmad Ampeng, Maklarin Lakim, Pazil Abdul-Patah, Anthony J Tosi, Markus Brameier, Dietmar Zinner and Christian Roos
    Citation: BMC Genomics 2015 16:222
    Content type: Research article Published on:

  29. The use of venom in intraspecific aggression is uncommon and venom-transmitting structures specifically used for intraspecific competition are found in few lineages of venomous taxa. Next-generation transcript...

    Authors: Jason Macrander, Mercer R Brugler and Marymegan Daly
    Citation: BMC Genomics 2015 16:221
    Content type: Research article Published on:

  30. There are over a half a million copies of L1 retroelements in the human genome which are responsible for as much as 0.5% of new human genetic diseases. Most new L1 inserts arise from young source elements that...

    Authors: Vincent A Streva, Vallmer E Jordan, Sara Linker, Dale J Hedges, Mark A Batzer and Prescott L Deininger
    Citation: BMC Genomics 2015 16:220
    Content type: Methodology article Published on:

  31. Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly deline...

    Authors: Ching-Hung Tseng, Pei-Wen Chiang, Hung-Chun Lai, Fuh-Kwo Shiah, Ting-Chang Hsu, Yi-Lung Chen, Liang-Saw Wen, Chun-Mao Tseng, Wung-Yang Shieh, Isaam Saeed, Saman Halgamuge and Sen-Lin Tang
    Citation: BMC Genomics 2015 16:219
    Content type: Research article Published on:

  32. Although Mycobacterium tuberculosis isolates are consisted of several different lineages and the epidemiology analyses are usually assessed relative to a particular reference genome, M. tuberculosis H37Rv, which ...

    Authors: Kayo Okumura, Masako Kato, Teruo Kirikae, Mitsunori Kayano and Tohru Miyoshi-Akiyama
    Citation: BMC Genomics 2015 16:218
    Content type: Research article Published on:

  33. Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean ada...

    Authors: Jiaoping Zhang, Qijian Song, Perry B Cregan, Randall L Nelson, Xianzhi Wang, Jixiang Wu and Guo-Liang Jiang
    Citation: BMC Genomics 2015 16:217
    Content type: Research article Published on:

  34. Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step toward...

    Authors: Huihui Li, Prashant Vikram, Ravi Prakash Singh, Andrzej Kilian, Jason Carling, Jie Song, Juan Andres Burgueno-Ferreira, Sridhar Bhavani, Julio Huerta-Espino, Thomas Payne, Deepmala Sehgal, Peter Wenzl and Sukhwinder Singh
    Citation: BMC Genomics 2015 16:216
    Content type: Research article Published on:

  35. Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT).

    Authors: Astrid L Basse, Karen Dixen, Rachita Yadav, Malin P Tygesen, Klaus Qvortrup, Karsten Kristiansen, Bjørn Quistorff, Ramneek Gupta, Jun Wang and Jacob B Hansen
    Citation: BMC Genomics 2015 16:215
    Content type: Research article Published on:

  36. Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Bi...

    Authors: Min Wang, Christine R Beck, Adam C English, Qingchang Meng, Christian Buhay, Yi Han, Harsha V Doddapaneni, Fuli Yu, Eric Boerwinkle, James R Lupski, Donna M Muzny and Richard A Gibbs
    Citation: BMC Genomics 2015 16:214
    Content type: Methodology article Published on:

  37. The editors of BMC Genomics would like to thank all our reviewers who have contributed to the journal in Volume 14 (2014).

    Authors: Derek E Anane
    Citation: BMC Genomics 2015 16:213
    Content type: Reviewer acknowledgement Published on:

  38. Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well a...

    Authors: Caitlyn Riedmann, Ye Ma, Manana Melikishvili, Steven Grason Godfrey, Zhou Zhang, Kuey Chu Chen, Eric C Rouchka and Yvonne N Fondufe-Mittendorf
    Citation: BMC Genomics 2015 16:212
    Content type: Research article Published on:

  39. The pistillody mutant wheat (Triticum aestivum L.) plant HTS-1 exhibits homeotic transformation of stamens into pistils or pistil-like structures. Unlike common wheat varieties, HTS-1 produces three to six pistil...

    Authors: Zaijun Yang, Zhengsong Peng, Shuhong Wei, Mingli Liao, Yan Yu and Zeyan Jang
    Citation: BMC Genomics 2015 16:211
    Content type: Research article Published on:

  40. Whole and partial chromosome losses or gains and structural chromosome changes are hallmarks of human tumors. Guanine-rich DNA, which has a potential to form a G-quadruplex (G4) structure, is particularly vulnera...

    Authors: Maja Tarailo-Graovac, Tammy Wong, Zhaozhao Qin, Stephane Flibotte, Jon Taylor, Donald G Moerman, Ann M Rose and Nansheng Chen
    Citation: BMC Genomics 2015 16:210
    Content type: Research article Published on:

  41. The Bacillus subtilis genome (BGM) vector is a novel cloning system based on the natural competence that enables B. subtilis to import extracellular DNA fragments into the cell and incorporate the recombinogenic ...

    Authors: Takafumi Ogawa, Tetsuo Iwata, Shinya Kaneko, Mitsuhiro Itaya and Junji Hirota
    Citation: BMC Genomics 2015 16:209
    Content type: Methodology article Published on:

  42. Tree peony (Paeonia section Moutan DC.) is known for its excellent ornamental and medicinal values. In 2011, seeds from P. ostii have been identified as novel resource of α-linolenic acid (ALA) for seed oil produ...

    Authors: Shan-Shan Li, Liang-Sheng Wang, Qing-Yan Shu, Jie Wu, Li-Guang Chen, Shuai Shao and Dan-Dan Yin
    Citation: BMC Genomics 2015 16:208
    Content type: Research article Published on:

  43. Thyroid cancer (TC) is the most common malignant cancer of the Endocrine System. Histologically, there are three main subtypes of TC: follicular, papillary and anaplastic. Diagnosing a thyroid tumor subtype wi...

    Authors: Jesús Espinal-Enríquez, Said Muñoz-Montero, Ivan Imaz-Rosshandler, Aldo Huerta-Verde, Carmen Mejía and Enrique Hernández-Lemus
    Citation: BMC Genomics 2015 16:207
    Content type: Research Article Published on:

  44. Chemical hybridization agents (CHAs) are often used to induce male sterility for the production of hybrid seeds. We previously discovered that monosulfuron ester sodium (MES), an acetolactate synthase (ALS) in...

    Authors: Zhanjie Li, Yufeng Cheng, Jianmin Cui, Peipei Zhang, Huixian Zhao and Shengwu Hu
    Citation: BMC Genomics 2015 16:206
    Content type: Research article Published on:

  45. Soil salinity is a significant factor that impairs plant growth and agricultural productivity, and numerous efforts are underway to enhance salt tolerance of economically important plants. Populus species are wid...

    Authors: Yazhen Ma, Ting Xu, Dongshi Wan, Tao Ma, Sheng Shi, Jianquan Liu and Quanjun Hu
    Citation: BMC Genomics 2015 16:205
    Content type: Database Published on:

  47. Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd+) is m...

    Authors: Wing Sze Ho, Hong-Yu Ou, Chew Chieng Yeo and Kwai Lin Thong
    Citation: BMC Genomics 2015 16:199
    Content type: Research article Published on:

  48. Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron stru...

    Authors: Yerbol Z Kurmangaliyev, Alexander V Favorov, Noha M Osman, Kjong-Van Lehmann, Daniel Campo, Matthew P Salomon, John Tower, Mikhail S Gelfand and Sergey V Nuzhdin
    Citation: BMC Genomics 2015 16:198
    Content type: Research article Published on:

  49. Methylation at arginine residues (R) is an important post-translational modification that regulates a myriad of essential cellular processes in eukaryotes, such as transcriptional regulation, RNA processing, s...

    Authors: Carlos E Hernando, Sabrina E Sanchez, Estefanía Mancini and Marcelo J Yanovsky
    Citation: BMC Genomics 2015 16:192
    Content type: Research article Published on:

  50. Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipel...

    Authors: Pradiptajati Kusuma, Murray P Cox, Denis Pierron, Harilanto Razafindrazaka, Nicolas Brucato, Laure Tonasso, Helena Loa Suryadi, Thierry Letellier, Herawati Sudoyo and François-Xavier Ricaut
    Citation: BMC Genomics 2015 16:191
    Content type: Research article Published on:

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BMC Genomics

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