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    Genome-wide imaging association study implicates functional activity and glial homeostasis of the caudate in smoking addiction.
    BMC Genomics 2017 Sep 19;18(1):740. Epub 2017 Sep 19.
    Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, 03756, USA.
    Background: Nearly 6 million deaths and over a half trillion dollars in healthcare costs worldwide are attributed to tobacco smoking each year. Extensive research efforts have been pursued to elucidate the molecular underpinnings of smoking addiction and facilitate cessation. In this study, we genotyped and obtained both resting state and task-based functional magnetic resonance imaging from 64 non-smokers and 42 smokers. Read More

    Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex.
    BMC Genomics 2017 Sep 18;18(1):735. Epub 2017 Sep 18.
    Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT, The Netherlands.
    Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Read More

    Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.
    BMC Genomics 2017 Sep 18;18(1):734. Epub 2017 Sep 18.
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia.
    Background: The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. Read More

    Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.
    BMC Genomics 2017 Sep 18;18(1):733. Epub 2017 Sep 18.
    Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
    Background: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana.

    Results: Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1. Read More

    5-hydroxymethylcytosine is highly dynamic across human fetal brain development.
    BMC Genomics 2017 Sep 18;18(1):738. Epub 2017 Sep 18.
    University of Exeter Medical School, RILD Building, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK.
    Background: Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory. Read More

    Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales.
    BMC Genomics 2017 Sep 18;18(1):736. Epub 2017 Sep 18.
    Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
    Background: Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. Read More

    Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor.
    BMC Genomics 2017 Sep 18;18(1):737. Epub 2017 Sep 18.
    INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France.
    Background: Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes. Read More

    A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map.
    BMC Genomics 2017 Sep 18;18(1):739. Epub 2017 Sep 18.
    Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
    Background: The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome.

    Results: We present a view at the molecular level of the normal human thyroid histology and physiology obtained by a systematic meta-analysis of all the available gene expression profiles for the whole organ. Read More

    Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche.
    BMC Genomics 2017 Sep 15;18(1):729. Epub 2017 Sep 15.
    State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
    Background: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. Read More

    The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.
    BMC Genomics 2017 Sep 15;18(1):730. Epub 2017 Sep 15.
    CIRAD, UMR AGAP, F-34398, Montpellier, France.
    Background: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Read More

    Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana.
    BMC Genomics 2017 Sep 16;18(1):731. Epub 2017 Sep 16.
    Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany.
    Background: During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. This is accompanied by dampened oscillations of circadian clock genes and disrupted oscillations of output genes and metabolites. During deacclimation in response to warm temperatures, cold acclimated plants lose freezing tolerance and resume growth and development. Read More

    Evolving DNA methylation and gene expression markers of B-cell chronic lymphocytic leukemia are present in pre-diagnostic blood samples more than 10 years prior to diagnosis.
    BMC Genomics 2017 Sep 13;18(1):728. Epub 2017 Sep 13.
    Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635, Athens, Greece.
    Background: B-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is not known what causes subjects with this condition to progress to CLL. Hence the discovery of prediagnostic markers has the potential to improve the identification of subjects likely to develop CLL and may also provide insights into the pathogenesis of the disease of potential clinical relevance. Read More

    Transcriptomic profiling of genes in matured dimorphic seeds of euhalophyte Suaeda salsa.
    BMC Genomics 2017 Sep 13;18(1):727. Epub 2017 Sep 13.
    Shandong Provincial Key Laboratory of Plant Stress, College of life science, Shandong Normal University, Jinan, Shandong, 250014, People's Republic of China.
    Background: Suaeda salsa (S. salsa) is a euhalophyte with high economic value. S. Read More

    Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages.
    BMC Genomics 2017 Sep 12;18(1):726. Epub 2017 Sep 12.
    Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Edificio TecLabs, Campus da FCUL, Campo Grande, 1749-016, Lisbon, Portugal.
    Background: Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infected wild boars (Sus scrofa). Read More

    Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.
    BMC Genomics 2017 Sep 12;18(1):721. Epub 2017 Sep 12.
    Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata, 700018, India.
    Background: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease.

    Result: We have studied gene co-expression network obtained from a PD-specific microarray data. Read More

    Comparative transcriptome analysis provides clues to molecular mechanisms underlying blue-green eggshell color in the Jinding duck (Anas platyrhynchos).
    BMC Genomics 2017 Sep 12;18(1):725. Epub 2017 Sep 12.
    College of Animal Science and Technology, Northwest A&F University, Xinong Road No.22, Yangling, Shaanxi, 712100, China.
    Background: In birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the paternal investment of males in the nest and eggs. However, little is known about its formation mechanisms. Read More

    Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.
    BMC Genomics 2017 Sep 12;18(1):724. Epub 2017 Sep 12.
    Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
    Background: Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns.

    Results: Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types. Read More

    Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.
    BMC Genomics 2017 Sep 12;18(1):722. Epub 2017 Sep 12.
    Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, ACT, Canberra, Australia.
    Background: Shigella flexneri is the primary cause of bacillary dysentery in the developing countries. S. flexneri serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. Read More

    Genome-wide gene expression analysis in the placenta from fetus with trisomy 21.
    BMC Genomics 2017 Sep 12;18(1):720. Epub 2017 Sep 12.
    Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, South Korea.
    Background: We performed whole human genome expression analysis in placenta tissue (normal and T21) samples in order to investigate gene expression into the pathogenesis of trisomy 21 (T21) placenta. We profiled the whole human genome expression of placental samples from normal and T21 fetuses using the GeneChip Human Genome U133 plus 2.0 array. Read More

    Regulatory network changes between cell lines and their tissues of origin.
    BMC Genomics 2017 Sep 12;18(1):723. Epub 2017 Sep 12.
    Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
    Background: Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin. Read More

    Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons.
    BMC Genomics 2017 Sep 11;18(1):716. Epub 2017 Sep 11.
    Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China.
    Background: Stegodyphus mimosarum is a candidate model organism belonging to the class Arachnida in the phylum Arthropoda. Studies on the biology of S. mimosarum over the past several decades have consisted of behavioral research and comparison of gene sequences based on the assembled genome sequence. Read More

    Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species.
    BMC Genomics 2017 Sep 11;18(1):711. Epub 2017 Sep 11.
    Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
    Background: MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species.

    Result: All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Read More

    De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly.
    BMC Genomics 2017 Sep 11;18(1):710. Epub 2017 Sep 11.
    Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA.
    Background: Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. Read More

    Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets.
    BMC Genomics 2017 Sep 11;18(1):719. Epub 2017 Sep 11.
    King's College London, Faculty of Life Sciences and Medicine, Diabetes and Nutritional Sciences, Metal Metabolism Group, 150 Stamford St, London, SE1 9NH, UK.
    Background: Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of transporters. However the ZIP paralogues of particular importance for zinc uptake, and associations with β-cell function and Type 2 Diabetes remain largely unexplored. Read More

    Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup.
    BMC Genomics 2017 Sep 11;18(1):717. Epub 2017 Sep 11.
    Tumor Immunology Laboratory, LIFE Center, University Clinic, Ludwig-Maximilians-University, Munich, Germany.
    Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. Read More

    Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes.
    BMC Genomics 2017 Sep 11;18(1):718. Epub 2017 Sep 11.
    Department of Medicine, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
    Background: The Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway has been well-characterized as a crucial signal transduction cascade that regulates vital biological responses including development, immunity and oncogenesis. Additionally to its canonical pathway that uses the phosphorylated form of the STAT transcription factor, recently the non-canonical pathway involving heterochromatin formation by unphosphorylated STAT was recently uncovered. Considering the significant role of the JAK/STAT pathway, we used the simple Drosophila system in which the non-canonical pathway was initially characterized, to compare putative canonical versus non-canonical transcriptional targets across the genome. Read More

    Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites.
    BMC Genomics 2017 Sep 11;18(1):715. Epub 2017 Sep 11.
    State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
    Background: The current chassis organisms or various types of cell factories have considerable advantages and disadvantages. Therefore, it is necessary to develop various chassis for an efficient production of different bioproducts from renewable resources. In this context, synthetic biology offers unique potentialities to produce value-added products of interests. Read More

    Determining the optimal number of independent components for reproducible transcriptomic data analysis.
    BMC Genomics 2017 Sep 11;18(1):712. Epub 2017 Sep 11.
    Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France.
    Background: Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. Read More

    The dynamic landscape of gene regulation during Bombyx mori oogenesis.
    BMC Genomics 2017 Sep 11;18(1):714. Epub 2017 Sep 11.
    Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, 400044, China.
    Background: Oogenesis in the domestic silkworm (Bombyx mori) is a complex process involving previtellogenesis, vitellogenesis and choriogenesis. During this process, follicles show drastic morphological and physiological changes. However, the genome-wide regulatory profiles of gene expression during oogenesis remain to be determined. Read More

    Integrated application of transcriptomics and metabolomics provides insights into glycogen content regulation in the Pacific oyster Crassostrea gigas.
    BMC Genomics 2017 Sep 11;18(1):713. Epub 2017 Sep 11.
    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
    Background: The Pacific oyster Crassostrea gigas is an important marine fishery resource, which contains high levels of glycogen that contributes to the flavor and the quality of the oyster. However, little is known about the molecular and chemical mechanisms underlying glycogen content differences in Pacific oysters. Using a homogeneous cultured Pacific oyster family, we explored these regulatory networks at the level of the metabolome and the transcriptome. Read More

    Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico.
    BMC Genomics 2017 Sep 8;18(1):707. Epub 2017 Sep 8.
    Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, OH, USA.
    Background: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. Read More

    Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense.
    BMC Genomics 2017 Sep 8;18(1):705. Epub 2017 Sep 8.
    State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
    Background: How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Read More

    Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma.
    BMC Genomics 2017 Sep 8;18(1):708. Epub 2017 Sep 8.
    Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
    Background: Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbations are triggered by inhalation of dust and microbial components. Affected animals eventually are unable of aerobic performance. Read More

    Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells.
    BMC Genomics 2017 Sep 8;18(1):706. Epub 2017 Sep 8.
    Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL, A1C 5S7, Canada.
    Background: Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. Therefore, the present study was conducted to determine if different levels of vegetable and fish oils can alter antiviral responses of salmon macrophage-like cells (MLCs). Atlantic salmon (Salmo salar) were fed diets containing 7. Read More

    Genome-wide association study reveals putative role of gga-miR-15a in controlling feed conversion ratio in layer chickens.
    BMC Genomics 2017 Sep 6;18(1):699. Epub 2017 Sep 6.
    National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
    Background: Efficient use of feed resources for farm animals is a critical concern in animal husbandry. Numerous genetic and nutritional studies have been conducted to investigate feed efficiency during the regular laying cycle of chickens. However, by prolonging the laying period of layers, the performance of feed utilization in the late-laying period becomes increasingly important. Read More

    De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi.
    BMC Genomics 2017 Sep 6;18(1):700. Epub 2017 Sep 6.
    Centre for Mediterranean Bioresources and Food (MeditBio), FCT, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
    Background: Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. Read More

    Lack of 14-3-3 proteins in Saccharomyces cerevisiae results in cell-to-cell heterogeneity in the expression of Pho4-regulated genes SPL2 and PHO84.
    BMC Genomics 2017 Sep 6;18(1):701. Epub 2017 Sep 6.
    Institute of Biology, Leiden University, Sylviusweg 72, NL-2333BE, Leiden, the Netherlands.
    Background: Ion homeostasis is an essential property of living organisms. The yeast Saccharomyces cerevisiae is an ideal model organism to investigate ion homeostasis at all levels. In this yeast genes involved in high-affinity phosphate uptake (PHO genes) are strongly induced during both phosphate and potassium starvation, indicating a link between phosphate and potassium homeostasis. Read More

    Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize.
    BMC Genomics 2017 Sep 6;18(1):702. Epub 2017 Sep 6.
    Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China.
    Background: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. Read More

    Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera.
    BMC Genomics 2017 Sep 6;18(1):698. Epub 2017 Sep 6.
    Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
    Background: Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae.

    Results: We determined complete or nearly complete mitogenomes of seven meloid species. Read More

    HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment.
    BMC Genomics 2017 Sep 5;18(1):694. Epub 2017 Sep 5.
    Center for Bioinformatics and Genomic Systems Engineering (CBGSE), 101 Gateway Blvd., College Station, TX, USA.
    Background: The information content of genomes plays a crucial role in the existence and proper development of living organisms. Thus, tremendous effort has been dedicated to developing DNA sequencing technologies that provide a better understanding of the underlying mechanisms of cellular processes. Advances in the development of sequencing technology have made it possible to sequence genomes in a relatively fast and inexpensive way. Read More

    A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri.
    BMC Genomics 2017 Sep 5;18(1):693. Epub 2017 Sep 5.
    Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
    Background: The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression.

    Results: Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Read More

    Patterns of host gene expression associated with harboring a foregut microbial community.
    BMC Genomics 2017 Sep 6;18(1):697. Epub 2017 Sep 6.
    Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.
    Background: Harboring foregut microbial communities is considered a key innovation that allows herbivorous mammals to colonize new ecological niches. However, the functions of these chambers have only been well studied at the molecular level in ruminants. Here, we investigate gene expression in the foregut chamber of herbivorous rodents and ask whether these gene expression patterns are consistent with results in ruminants. Read More

    Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato.
    BMC Genomics 2017 Sep 6;18(1):695. Epub 2017 Sep 6.
    Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.
    Background: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). Read More

    Dual transcriptome of the immediate neutrophil and Candida albicans interplay.
    BMC Genomics 2017 Sep 6;18(1):696. Epub 2017 Sep 6.
    Department of Clinical Microbiology, Umeå Centre for Microbial Research (UCMR) & Laboratory of Molecular Infection Medicine Sweden (MIMS), Umeå University, Umea, Sweden.
    Background: Neutrophils are traditionally considered transcriptionally inactive. Compared to other immune cells, little is known about their transcriptional profile during interaction with pathogens.

    Methods: We analyzed the meta-transcriptome of the neutrophil-Candida albicans interplay and the transcriptome of C. Read More

    Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.
    BMC Genomics 2017 Sep 4;18(1):684. Epub 2017 Sep 4.
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
    Background: Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA clones. Most MRSA lineages show an association with specific MGEs and the evolution of MGE composition following clonal expansion has not been widely studied.

    Results: We investigated the genomes of 1193 S. Read More

    Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.
    BMC Genomics 2017 Sep 5;18(1):686. Epub 2017 Sep 5.
    Institute of Biology, Molecular Parasitology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 14, 10115, Berlin, Germany.
    Background: Parasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized ("hard wired") program of infection. Assuming that large-scale functional plasticity would be discernible in the parasite transcriptome we have performed a dual RNA-seq study of the lifecycle of Eimeria falciformis using infected mice with different immune status as models for coccidian infections.

    Results: We compared parasite and host transcriptomes (dual transcriptome) between naïve and challenge infected mice, as well as between immune competent and immune deficient ones. Read More

    Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken.
    BMC Genomics 2017 Sep 5;18(1):687. Epub 2017 Sep 5.
    Department of Animal Science, North Carolina State University, Polk Hall 232D, Box 7621, Raleigh, NC, 27695, USA.
    Background: The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for the chick to successfully transition from the metabolism of stored egg yolk to the utilization of carbohydrate-based feed. However, regulation of this metabolic switch is not well understood. Read More

    Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.
    BMC Genomics 2017 Sep 4;18(1):683. Epub 2017 Sep 4.
    Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan.
    Background: Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. Read More

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