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  1. Research article

    High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

    Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and qu...

    Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A. El-Kassaby and Hui Chen

    BMC Genomics 2017 18:546

    Published on: 20 July 2017

  2. Research article

    Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

    The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and i...

    Irina Ćalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John E. Carlson and David B. Neale

    BMC Genomics 2017 18:547

    Published on: 20 July 2017

  3. Research article

    Identification and characterization of long non-coding RNAs in subcutaneous adipose tissue from castrated and intact full-sib pair Huainan male pigs

    Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male ...

    Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao and Baosong Xing

    BMC Genomics 2017 18:542

    Published on: 19 July 2017

  4. Methodology article

    Hybrid assembly with long and short reads improves discovery of gene family expansions

    Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.

    Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G. Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz…

    BMC Genomics 2017 18:541

    Published on: 19 July 2017

  5. Research article

    Genome analysis of E. coli isolated from Crohn’s disease patients

    Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was cont...

    Daria V. Rakitina, Alexander I. Manolov, Alexandra V. Kanygina, Sofya K. Garushyants, Julia P. Baikova, Dmitry G. Alexeev, Valentina G. Ladygina, Elena S. Kostryukova, Andrei K. Larin, Tatiana A. Semashko, Irina Y. Karpova, Vladislav V. Babenko, Ruzilya K. Ismagilova, Sergei Y. Malanin, Mikhail S. Gelfand, Elena N. Ilina…

    BMC Genomics 2017 18:544

    Published on: 19 July 2017

  6. Research article

    Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous

    The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their act...

    Pamela Córdova, Ana-María Gonzalez, David R. Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes and Jennifer Alcaíno

    BMC Genomics 2017 18:540

    Published on: 19 July 2017

  7. Methodology article

    A permutation-based non-parametric analysis of CRISPR screen data

    Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or a...

    Gaoxiang Jia, Xinlei Wang and Guanghua Xiao

    BMC Genomics 2017 18:545

    Published on: 19 July 2017

  8. Research article

    Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

    Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of ...

    Colleen P. MacMillan, Hannah Birke, Aaron Chuah, Elizabeth Brill, Yukiko Tsuji, John Ralph, Elizabeth S. Dennis, Danny Llewellyn and Filomena A. Pettolino

    BMC Genomics 2017 18:539

    Published on: 18 July 2017

  9. Software

    COGNATE: comparative gene annotation characterizer

    The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization...

    Jeanne Wilbrandt, Bernhard Misof and Oliver Niehuis

    BMC Genomics 2017 18:535

    Published on: 17 July 2017

  10. Research article

    Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression

    The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are respon...

    Lauren E. Gonzalez, Kristen Keller, Karen X. Chan, Megan M. Gessel and Bryan C. Thines

    BMC Genomics 2017 18:533

    Published on: 17 July 2017

  11. Research article

    Evolutionary and genetic analysis of the VP2 gene of canine parvovirus

    Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar ...

    Gairu Li, Senlin Ji, Xiaofeng Zhai, Yuxiang Zhang, Jie Liu, Mengyan Zhu, Jiyong Zhou and Shuo Su

    BMC Genomics 2017 18:534

    Published on: 17 July 2017

  12. Methodology article

    Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

    Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation o...

    Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze and Olivier Panaud

    BMC Genomics 2017 18:537

    Published on: 17 July 2017

  13. Research article

    Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis

    Histone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in eth...

    Likai Wang, Fan Zhang, Siddharth Rode, Kevin K. Chin, Eun Esther Ko, Jonghwan Kim, Vishwanath R. Iyer and Hong Qiao

    BMC Genomics 2017 18:538

    Published on: 17 July 2017

  14. Research article

    Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828

    The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to ...

    Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Md. Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan and Alistair D. M. Dove

    BMC Genomics 2017 18:532

    Published on: 14 July 2017

  15. Research article

    Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery

    Tuberculosis (TB) is caused by Mycobacterium tuberculosis and represents one of the major challenges facing drug discovery initiatives worldwide. The considerable rise in bacterial drug resistance in recent years...

    Amine Namouchi, Mena Cimino, Sandrine Favre-Rochex, Patricia Charles and Brigitte Gicquel

    BMC Genomics 2017 18:530

    Published on: 13 July 2017

  16. Research article

    Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns

    Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in i...

    Katherine H. Tanaka, Antony T. Vincent, Jean-Guillaume Emond-Rheault, Marcin Adamczuk, Michel Frenette and Steve J. Charette

    BMC Genomics 2017 18:528

    Published on: 12 July 2017

  17. Research article

    Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses

    Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association s...

    Long Yan, Nicolle Hofmann, Shuxian Li, Marcio Elias Ferreira, Baohua Song, Guoliang Jiang, Shuxin Ren, Charles Quigley, Edward Fickus, Perry Cregan and Qijian Song

    BMC Genomics 2017 18:529

    Published on: 12 July 2017

  18. Methodology Article

    Scaffolding of long read assemblies using long range contact information

    Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually do...

    Jay Ghurye, Mihai Pop, Sergey Koren, Derek Bickhart and Chen-Shan Chin

    BMC Genomics 2017 18:527

    Published on: 12 July 2017

  19. Research article

    Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study

    An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks ...

    Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M. Earl and Carlos Caldas

    BMC Genomics 2017 18:526

    Published on: 11 July 2017

  20. Research article

    Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

    The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted ...

    Bárbara S. F. Müller, Leandro G. Neves, Janeo E. de Almeida Filho, Márcio F. R. Resende Jr, Patricio R. Muñoz, Paulo E. T. dos Santos, Estefano Paludzyszyn Filho, Matias Kirst and Dario Grattapaglia

    BMC Genomics 2017 18:524

    Published on: 11 July 2017

  21. Research article

    Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

    A restricted set of aerobic bacteria dominated by the Acinetobacter genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they prot...

    Azadeh Saffarian, Marie Touchon, Céline Mulet, Régis Tournebize, Virginie Passet, Sylvain Brisse, Eduardo P. C. Rocha, Philippe J. Sansonetti and Thierry Pédron

    BMC Genomics 2017 18:525

    Published on: 11 July 2017

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