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    10592 results match your criteria BMC Genomics [Journal]

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    A-GAME: improving the assembly of pooled functional metagenomics sequence data.
    BMC Genomics 2018 Jan 12;19(1):44. Epub 2018 Jan 12.
    Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.
    Background: Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications. Read More

    Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance.
    BMC Genomics 2018 Jan 12;19(1):40. Epub 2018 Jan 12.
    Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354, South Korea.
    Background: Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms.

    Results: We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter. Read More

    Correction to: Relatively frequent switching of transcription start sites during cerebellar development.
    BMC Genomics 2018 Jan 11;19(1):39. Epub 2018 Jan 11.
    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
    Correction: The authors of the original article [1] would like to recognize the critical contribution of core members of the FANTOM5 Consortium, who played the critical role of HeliScopeCAGE sequencing experiments, quality control of tag reads and processing of the raw sequencing data. Read More

    A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence.
    BMC Genomics 2018 Jan 10;19(1):37. Epub 2018 Jan 10.
    Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National & Kapodistrian University of Athens, 75 Mikras Asias St, GR-11527, Athens, Greece.
    Background: Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that needs to be circumvented for cancer to progress. Micro-RNAs, a subclass of regulatory, non-coding RNAs, participate in senescence regulation. Read More

    Expression of Vimentin in hair follicle growth cycle of inner Mongolian Cashmere goats.
    BMC Genomics 2018 Jan 10;19(1):38. Epub 2018 Jan 10.
    College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
    Background: The growth of Inner Mongolian Cashmere goat skin hair follicle exhibits a periodic growth pattern. The hair growth cycle is distinguished as telogen, anagen, and catagen stages. The role of vimentin in the growth process of hair follicles is evident. Read More

    Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice.
    BMC Genomics 2018 Jan 10;19(1):35. Epub 2018 Jan 10.
    School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, Fujian, 363000, China.
    Background: The cytochrome P450 monooxygenases (CYP450, CYP, P450) catalyze numerous monooxygenation/hydroxylation reactions in biochemical pathways. Although CYP superfamily has been systematically studied in a few species, the genome-scale research about it in rice has not been done.

    Results: In this study, a total of 355 CYPs encoded by 326 genes were identified in japonica genome. Read More

    Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle.
    BMC Genomics 2018 Jan 9;19(1):34. Epub 2018 Jan 9.
    Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.
    Background: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Read More

    De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species.
    BMC Genomics 2018 Jan 8;19(1):32. Epub 2018 Jan 8.
    Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.
    Background: Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Read More

    Insights into teleost sex determination from the Seriola dorsalis genome assembly.
    BMC Genomics 2018 Jan 8;19(1):31. Epub 2018 Jan 8.
    Genome Informatics Facility, Iowa State University, 206 Science I, Ames, IA, 50011, USA.
    Background: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production. Read More

    Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing.
    BMC Genomics 2018 Jan 8;19(1):30. Epub 2018 Jan 8.
    Center for Cancer Genome Discovery, DFCI, 450 Brookline Avenue, Dana840b, Boston, MA, 02215, USA.
    Background: Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.

    Results: Cross-talk rates up to 0. Read More

    Proteomics reveals changes in hepatic proteins during chicken embryonic development: an alternative model to study human obesity.
    BMC Genomics 2018 Jan 8;19(1):29. Epub 2018 Jan 8.
    Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
    Background: Chicken embryos are widely used as a model for studies of obesity; however, no detailed information is available about the dynamic changes of proteins during the regulation of adipose biology and metabolism. Thus, the present study used an isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic approach to identify the changes in protein abundance at different stages of chicken embryonic development.

    Results: In this study, the abundances of 293 hepatic proteins in 19-day old of chicken embryos compared with 14-day old and 160 hepatic proteins at hatching compared with 19-day old embryos were significantly changed. Read More

    Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.
    BMC Genomics 2018 Jan 8;19(1):33. Epub 2018 Jan 8.
    APC Microbiome Institute, University College Cork, Cork, Ireland.
    Background: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. Read More

    A-to-I RNA editing in the rat brain is age-dependent, region-specific and sensitive to environmental stress across generations.
    BMC Genomics 2018 Jan 8;19(1):28. Epub 2018 Jan 8.
    Department of Psychology, University of Haifa, Haifa, Israel.
    Background: Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluidics-based multiplex PCR sequencing (mmPCR-seq) technique to assess the effects of development and environmental stress on A-to-I editing at 146 pre-selected, conserved sites in the rat prefrontal cortex and amygdala. Furthermore, we asked whether changes in editing can be observed in offspring of stress-exposed rats. Read More

    Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion.
    BMC Genomics 2018 Jan 6;19(1):26. Epub 2018 Jan 6.
    FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
    Background: Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protecting papaya from herbivorous insects. Except the four major PLCPs purified and characterized in papaya latex, the rest of the PLCPs in papaya genome are largely unknown. Read More

    Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower.
    BMC Genomics 2018 Jan 6;19(1):27. Epub 2018 Jan 6.
    Istituto per la Protezione Sostenibile delle Piante, CNR-IPSP, Via Università 133, 80055, Portici (Naples), Italy.
    Background: The early phases of Diaporthe helianthi pathogenesis on sunflower are characterized by the production of phytotoxins that may play a role in host colonisation. In previous studies, phytotoxins of a polyketidic nature were isolated and purified from culture filtrates of virulent strains of D. helianthi isolated from sunflower. Read More

    Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts.
    BMC Genomics 2018 Jan 5;19(1):19. Epub 2018 Jan 5.
    CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
    Background: Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. Read More

    Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.
    BMC Genomics 2018 Jan 6;19(1):25. Epub 2018 Jan 6.
    Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Milan, Segrate-Milan, Italy.
    Background: Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functional genomic studies. Read More

    The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains.
    BMC Genomics 2018 Jan 5;19(1):20. Epub 2018 Jan 5.
    Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
    Background: Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity.

    Results: Here we report the finalized genome sequence of the environmental strain Aeromonas salmonicida subsp. Read More

    Exploring the relationship between intron retention and chromatin accessibility in plants.
    BMC Genomics 2018 Jan 5;19(1):21. Epub 2018 Jan 5.
    Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA.
    Background: Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. Read More

    RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.
    BMC Genomics 2018 Jan 6;19(1):24. Epub 2018 Jan 6.
    IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
    Background: The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Read More

    Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root.
    BMC Genomics 2018 Jan 5;19(1):23. Epub 2018 Jan 5.
    Department of Biology, University of Saskatchewan, Saskatoon, S7N 5E2, Canada.
    Background: Clubroot is an important disease caused by the obligate parasite Plasmodiophora brassicae that infects the Brassicaceae. As a soil-borne pathogen, P. brassicae induces the generation of abnormal tissue in the root, resulting in the formation of galls. Read More

    A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci.
    BMC Genomics 2018 Jan 5;19(1):18. Epub 2018 Jan 5.
    Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
    Background: Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Read More

    Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies.
    BMC Genomics 2018 Jan 5;19(1):22. Epub 2018 Jan 5.
    Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
    Background: Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. Read More

    Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum.
    BMC Genomics 2018 Jan 4;19(1):15. Epub 2018 Jan 4.
    State Key Laboratory of Crop Genetics & Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
    Background: We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. Read More

    Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains.
    BMC Genomics 2018 Jan 4;19(1):16. Epub 2018 Jan 4.
    Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36830, USA.
    Background: Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. Read More

    Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral.
    BMC Genomics 2018 Jan 4;19(1):17. Epub 2018 Jan 4.
    Department of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA.
    Background: Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization.

    Results: Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are "primed" for settlement. Read More

    Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase.
    BMC Genomics 2018 Jan 3;19(1). Epub 2018 Jan 3.
    Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
    Background: Human induced pluripotent stem cells (hiPSCs) have been attempted for clinical application with diverse iPSCs sources derived from various cell types. This proposes that there would be a shared reprogramming route regardless of different starting cell types. However, the insights of reprogramming process are mostly restricted to only fibroblasts of both human and mouse. Read More

    Global accumulation of circRNAs during aging in Caenorhabditis elegans.
    BMC Genomics 2018 Jan 3;19(1). Epub 2018 Jan 3.
    University of Nevada, Reno, Department of Biology, 1664 N. Virginia St, Reno, NV, 89557, USA.
    Background: Circular RNAs (CircRNAs) are a newly appreciated class of RNAs that lack free 5' and 3' ends, are expressed by the thousands in diverse forms of life, and are mostly of enigmatic function. Ostensibly due to their resistance to exonucleases, circRNAs are known to be exceptionally stable. Previous work in Drosophila and mice have shown that circRNAs increase during aging in neural tissues. Read More

    The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna.
    BMC Genomics 2018 Jan 3;19(1):12. Epub 2018 Jan 3.
    Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 26, 14476, Potsdam, Germany.
    Background: The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. Read More

    The variome of pneumococcal virulence factors and regulators.
    BMC Genomics 2018 Jan 3;19(1):10. Epub 2018 Jan 3.
    Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, Ernst-Moritz-Arndt University of Greifswald, Felix-Hausdorff-Str. 8, D-17487, Greifswald, Germany.
    Background: In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target proteins to be included in a vaccine formulation have to accomplish several genetic and immunological characteristics, (such as conservation, distribution, immunogenicity and protective effect), in order to ensure its suitability and effectiveness. This study aimed to get comprehensive insights into the genomic organization, population distribution and genetic conservation of all pneumococcal surface-exposed proteins, genetic regulators and other virulence factors, whose important function and role in pathogenesis has been demonstrated or hypothesized. Read More

    A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees.
    BMC Genomics 2018 Jan 3;19(1):11. Epub 2018 Jan 3.
    Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.
    Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32-38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri. Read More

    Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.
    BMC Genomics 2018 Jan 3;19(1):14. Epub 2018 Jan 3.
    Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden.
    Background: Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. Read More

    No association between ACTN3 R577X and ACE I/D polymorphisms and endurance running times in 698 Caucasian athletes.
    BMC Genomics 2018 Jan 3;19(1):13. Epub 2018 Jan 3.
    Institute of Sport, Exercise and Active Living (ISEAL), Victoria University, Victoria, Australia.
    Background: Studies investigating associations between ACTN3 R577X and ACE I/D genotypes and endurance athletic status have been limited by small sample sizes from mixed sport disciplines and lack quantitative measures of performance.

    Aim: To examine the association between ACTN3 R577X and ACE I/D genotypes and best personal running times in a large homogeneous cohort of endurance runners.

    Methods: We collected a total of 1064 personal best 1500, 3000, 5000 m and marathon running times of 698 male and female Caucasian endurance athletes from six countries (Australia, Greece, Italy, Poland, Russia and UK). Read More

    Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton.
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China.
    Background: Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. Read More

    Identification of 74 cytochrome P450 genes and co-localized cytochrome P450 genes of the CYP2K, CYP5A, and CYP46A subfamilies in the mangrove killifish Kryptolebias marmoratus.
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
    Background: The mangrove killifish Kryptolebias marmoratus is the only vertebrate that reproduces by self-fertilizing and is an important model species in genetics and marine ecotoxicology. Using whole-genome and transcriptome sequences, we identified all members of the cytochrome P450 (CYP) family in this model teleost and compared them with those of other teleosts.

    Results: A total of 74 cytochrome P450 genes and one pseudogene were identified in K. Read More

    Acyl-CoA-binding protein family members in laticifers are possibly involved in lipid and latex metabolism of Hevea brasiliensis (the Para rubber tree).
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.
    Background: Acyl-CoA-binding proteins (ACBPs) are mainly involved in acyl-CoA ester binding and trafficking in eukaryotic cells, and their various functions have been characterized in model plants, such as Arabidopsis thaliana (A. thaliana), Oryza sativa (rice), and other plant species. In the present study, genome-wide mining and expression analysis of ACBP genes was performed on Hevea brasiliensis (the para rubber tree), the most important latex-producing crop in the world. Read More

    Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea.
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
    Background: Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically increased worldwide demand due to its numerous health benefits. Genetic markers can facilitate the selection of berries with desirable climatic adaptations, agronomic and nutritious characteristics to improve cultivation programs. Read More

    Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates.
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay.
    Background: Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%). Read More

    Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii.
    BMC Genomics 2018 Jan 2;19(1). Epub 2018 Jan 2.
    Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, Sichuan province, 611130, People's Republic of China.
    Background: Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. Read More

    Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum.
    BMC Genomics 2017 12 29;18(1):1000. Epub 2017 Dec 29.
    College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
    Background: Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Read More

    Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants.
    BMC Genomics 2017 12 29;18(1):995. Epub 2017 Dec 29.
    Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
    Background: Lipopolysaccharide (LPS) from Gram-negative bacteria cause innate immune responses in animals and plants. The molecules involved in LPS signaling in animals are well studied, whereas those in plants are not yet as well documented. Recently, we identified Arabidopsis AtLBR-2, which binds to LPS from Pseudomonas aeruginosa (pLPS) directly and regulates pLPS-induced defense responses, such as pathogenesis-related 1 (PR1) expression and reactive oxygen species (ROS) production. Read More

    Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.
    BMC Genomics 2017 12 29;18(1):999. Epub 2017 Dec 29.
    Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland.
    Background: Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. Read More

    Multiple functions of CREB-binding protein during postembryonic development: identification of target genes.
    BMC Genomics 2017 12 29;18(1):996. Epub 2017 Dec 29.
    Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY, 40546, USA.
    Background: Juvenile hormones (JH) and ecdysteroids control postembryonic development in insects. They serve as valuable targets for pest management. Hence, understanding the molecular mechanisms of their action is of crucial importance. Read More

    The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.
    BMC Genomics 2017 12 29;18(1):997. Epub 2017 Dec 29.
    Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
    Background: The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Read More

    Profiling the onset of somatic embryogenesis in Arabidopsis.
    BMC Genomics 2017 12 29;18(1):998. Epub 2017 Dec 29.
    Insitut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA, Route de St-Cyr (RD10), 78026, Versailles Cedex, France.
    Background: Totipotency is the ability of a cell to regenerate a whole organism. Plant somatic embryogenesis (SE) is a remarkable example of totipotency because somatic cells reverse differentiation, respond to an appropriate stimulus and initiate embryo development. Although SE is an ideal system to investigate de-differentiation and differentiation, we still lack a deep molecular understanding of the phenomenon due to experimental restraints. Read More

    Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome.
    BMC Genomics 2017 12 28;18(1):989. Epub 2017 Dec 28.
    Department of Animal Science, Iowa State University, Ames, IA, USA.
    Background: Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. Read More

    Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders.
    BMC Genomics 2017 12 28;18(1):992. Epub 2017 Dec 28.
    Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA.
    Background: Mitochondria are the site of the citric acid cycle and oxidative phosphorylation (OXPHOS). In metazoans, the mitochondrial genome is a small, circular molecule averaging 16.5 kb in length. Read More

    Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.
    BMC Genomics 2017 12 28;18(1):993. Epub 2017 Dec 28.
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
    Background: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. Read More

    Transcriptional effects of a positive feedback circuit in Drosophila melanogaster.
    BMC Genomics 2017 12 28;18(1):990. Epub 2017 Dec 28.
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
    Background: Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited via dietary tetracycline. Although insects carrying tTAV fail to survive until adulthood in the absence of tetracycline, the exact reason for its lethality, as well as the transcriptomic effects of an active positive feedback circuit, remain unknown. Read More

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