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    Comparison of normalization methods for the analysis of metagenomic gene abundance data.
    BMC Genomics 2018 Apr 20;19(1):274. Epub 2018 Apr 20.
    Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96, Gothenburg, Sweden.
    Background: In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Read More

    Genomic regions responsible for seminal and crown root lengths identified by 2D & 3D root system image analysis.
    BMC Genomics 2018 Apr 20;19(1):273. Epub 2018 Apr 20.
    Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada.
    Background: Genetic improvement of root system architecture is a promising approach for improved uptake of water and mineral nutrients distributed unevenly in the soil. To identify genomic regions associated with the length of different root types in rice, we quantified root system architecture in a set of 26 chromosome segment substitution lines derived from a cross between lowland indica rice, IR64, and upland tropical japonica rice, Kinandang Patong, (IK-CSSLs), using 2D & 3D root phenotyping platforms.

    Results: Lengths of seminal and crown roots in the IK-CSSLs grown under hydroponic conditions were measured by 2D image analysis (RootReader2D). Read More

    Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular.
    BMC Genomics 2018 Apr 20;19(1):276. Epub 2018 Apr 20.
    Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK.
    Background: Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. Read More

    Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements.
    BMC Genomics 2018 Apr 20;19(1):275. Epub 2018 Apr 20.
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
    Background: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. Read More

    Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes.
    BMC Genomics 2018 Apr 19;19(1):271. Epub 2018 Apr 19.
    USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA.
    Background: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. Read More

    Indel detection from DNA and RNA sequencing data with transIndel.
    BMC Genomics 2018 Apr 19;19(1):270. Epub 2018 Apr 19.
    Masonic Cancer Center, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA.
    Background: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data.

    Results: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data. Read More

    Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum.
    BMC Genomics 2018 Apr 19;19(1):269. Epub 2018 Apr 19.
    Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
    Background: The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. Read More

    Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence.
    BMC Genomics 2018 Apr 18;19(1):265. Epub 2018 Apr 18.
    CBGP UMR 1062, INRA-IRD-CIRAD-Montpellier SupAgro, Montferrier sur Lez, Montpellier, France.
    Background: Most phytophagous insects have morphological, behavioral and physiological adaptations allowing them to specialize on one or a few plant species. Identifying the mechanisms involved in host plant specialization is crucial to understand the role of divergent selection between different environments in species diversification, and to identify sustainable targets for the management of insect pest species. In the present study, we measured larval phenotypic and transcriptomic responses to host plants in two related phytophagous lepidopteran species: the European corn borer (ECB), a worldwide pest of maize, and the adzuki bean borer (ABB), which feeds of various dicotyledons. Read More

    Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera).
    BMC Genomics 2018 Apr 18;19(1):264. Epub 2018 Apr 18.
    Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
    Background: Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. Read More

    Identification of two different chemosensory pathways in representatives of the genus Halomonas.
    BMC Genomics 2018 Apr 18;19(1):266. Epub 2018 Apr 18.
    Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina.
    Background: Species of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examined the genome of a Halomonas isolate from a hydrocarbon-contaminated site to search for chemosensory genes that might be responsible for the observed chemotactic behavior of this organism as well as for other responses to environmental cues.

    Results: Using genome-wide comparative tools, our isolate was identified as a strain of Halomonas titanicae (strain KHS3), together with two other Halomonas strains with available genomes that had not been previously identified at a species level. Read More

    Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models.
    BMC Genomics 2018 Apr 18;19(1):267. Epub 2018 Apr 18.
    National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.
    Background: The characterization of genomic or epigenomic variation in human and animal models could provide important insight into pathophysiological mechanisms of various diseases, and lead to new developments in disease diagnosis and clinical intervention. The African green monkey (AGM; Chlorocebus aethiops) and cynomolgus monkey (CM; Macaca fascicularis) have long been considered important animal models in biomedical research. However, non-human primate-specific methods applicable to epigenomic analyses in AGM and CM are lacking. Read More

    Correction to: Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure.
    BMC Genomics 2018 Apr 18;19(1):268. Epub 2018 Apr 18.
    Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
    After publication of the original article [1] the authors noted that the key displayed in Figure 1a was incorrect, as the PMA and HgCl2 conditions had been switched. Read More

    A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing.
    BMC Genomics 2018 Apr 17;19(1):263. Epub 2018 Apr 17.
    Color Genomics, 831 Mitten Road, Burlingame, CA, 94010, USA.
    Background: Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. With recent advances in NGS technology and software tools, the majority of variants called using NGS alone are in fact accurate and reliable. Read More

    Correction to: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls.
    BMC Genomics 2018 Apr 17;19(1):261. Epub 2018 Apr 17.
    CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia.
    Upon publication of the original article [1], the authors had flagged that Fig. 1 had been published twice, as both Fig. 1 and Additional file 3. Read More

    Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation.
    BMC Genomics 2018 Apr 17;19(1):262. Epub 2018 Apr 17.
    CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China.
    Background: Neuron maturation is a critical process in neurogenesis, during which neurons gain their morphological, electrophysiological and molecular characteristics for their functions as the central components of the nervous system.

    Results: To better understand the molecular changes during this process, we combined the protein-protein interaction network and public single cell RNA-seq data of mature and immature neurons to identify functional modules relevant to the neuron maturation process in humans. Among the 109 functional modules in total, 33 showed significant gene expression level changes (discriminating modules) which participate in varied functions including energy consumption, synaptic functions and housekeeping functions such as translation and splicing. Read More

    A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.
    BMC Genomics 2018 Apr 16;19(1):257. Epub 2018 Apr 16.
    The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.
    Background: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Read More

    Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations.
    BMC Genomics 2018 Apr 16;19(1):254. Epub 2018 Apr 16.
    Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
    Background: Plasmodiophora brassicae is a soilborne pathogen of the family Brassicaceae and the causal agent of clubroot disease. In Canada, P. brassicae is now one of the most important constraints to canola (Brassica napus) production, and is managed mainly by the deployment of resistant cultivars. Read More

    Slow darkening of pinto bean seed coat is associated with significant metabolite and transcript differences related to proanthocyanidin biosynthesis.
    BMC Genomics 2018 Apr 16;19(1):260. Epub 2018 Apr 16.
    London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
    Background: Postharvest seed coat darkening in pinto bean is an undesirable trait resulting in a loss in the economic value of the crop. The extent of darkening varies between the bean cultivars and their storage conditions.

    Results: Metabolite analysis revealed that the majority of flavonoids including proanthocyanidin monomer catechin accumulated at higher level in a regular darkening (RD) pinto line CDC Pintium than in a slow darkening (SD) line 1533-15. Read More

    Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization.
    BMC Genomics 2018 Apr 16;19(1):259. Epub 2018 Apr 16.
    National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.
    Background: Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. Read More

    1000 human genomes carry widespread signatures of GC biased gene conversion.
    BMC Genomics 2018 Apr 16;19(1):256. Epub 2018 Apr 16.
    Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH, 43614, USA.
    Background: GC-Biased Gene Conversion (gBGC) is one of the important theories put forward to explain profound long-range non-randomness in nucleotide compositions along mammalian chromosomes. Nucleotide changes due to gBGC are hard to distinguish from regular mutations. Here, we present an algorithm for analysis of millions of known SNPs that detects a subset of so-called "SNP flip-over" events representing recent gBGC nucleotide changes, which occurred in previous generations via non-crossover meiotic recombination. Read More

    Transcriptome analysis of granulosa cells after conventional vs long FSH-induced superstimulation in cattle.
    BMC Genomics 2018 Apr 16;19(1):258. Epub 2018 Apr 16.
    Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada.
    Background: Prolongation of superstimulatory treatment appears to be associated with a greater superovulatory response and with greater oocyte maturation in cattle. A genome-wide bovine oligo-microarray was used to compare the gene expression of granulosa cells collected from ovarian follicles after differing durations of the growing phase induced by exogenous FSH treatment. Cows were given a conventional (4-day) or long (7-day) superstimulatory treatment (25 mg FSH im at 12-h intervals; n = 6 per group), followed by prostaglandin treatment with last FSH and LH treatment 24 h later. Read More

    Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry.
    BMC Genomics 2018 Apr 16;19(1):253. Epub 2018 Apr 16.
    Department of Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
    Background: It has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced transport capacity of dietary lipids. However, in-depth ontogenetic analysis of intestinal PL and LP synthesis with the development of salmon has yet to be performed. Therefore, in this paper we used RNA-Seq technology to investigate the expression of genes involved in PL synthesis and LP formation throughout early developmental stages and associate insufficient expression of synthesis pathways in salmon fry with its higher dietary PL requirement. Read More

    Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content.
    BMC Genomics 2018 Apr 16;19(1):255. Epub 2018 Apr 16.
    Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
    Background: Brassica crops are cultivated widely for human consumption and animal feed purposes, and oilseed rape/canola (Brassica napus and rapa) is the second most important oilseed worldwide. Because of its natural diversity and genetic complexity, genomics studies on oilseed rape will be a useful resource base to modify the quantity and quality of biomass in various crops, and therefore, should have a positive impact on lignocellulosic biofuel production. The objective of this study was to perform microarray analysis on two variable lignin containing oilseed rape cultivars to target novel genes and transcription factors of importance in Brassica lignin regulation for applied research. Read More

    A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.
    BMC Genomics 2018 Apr 13;19(1):250. Epub 2018 Apr 13.
    Earlham Institute, Norwich research Park, Norwich, UK.
    Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Read More

    Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress.
    BMC Genomics 2018 Apr 13;19(1):251. Epub 2018 Apr 13.
    Ministry of Education, Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Qingdao, 266003, China.
    Background: Pyropia yezoensis, a marine red alga, is an ideal research model for studying the mechanisms of abiotic stress tolerance in intertidal seaweed. Real-time quantitative polymerase chain reaction (RT-qPCR) is the most commonly used method to analyze gene expression levels. To accurately quantify gene expression, selection and validation of stable reference genes is required. Read More

    Correction to: An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes.
    BMC Genomics 2018 Apr 11;19(1):245. Epub 2018 Apr 11.
    Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
    ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. Read More

    Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution.
    BMC Genomics 2018 Apr 11;19(1):247. Epub 2018 Apr 11.
    Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA.
    Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii's genome contains an abundance of pseudogenes and numerous selfish genetic elements. Read More

    Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine.
    BMC Genomics 2018 Apr 11;19(1):248. Epub 2018 Apr 11.
    Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F- 33140, Villenave d'Ornon, France.
    Background: The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family's tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Read More

    Comparative transcriptome analysis of hypothalamus-regulated feed intake induced by exogenous visfatin in chicks.
    BMC Genomics 2018 Apr 11;19(1):249. Epub 2018 Apr 11.
    College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
    Background: The intracerebroventricular injection of visfatin increases feed intake. However, little is known about the molecular mechanism in chicks. This study was conducted to assess the effect of visfatin on the feeding behavior of chicks and the associated molecular mechanism. Read More

    A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals.
    BMC Genomics 2018 Apr 11;19(1):246. Epub 2018 Apr 11.
    College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.
    Background: Glucose plays a key role as an energy source in most mammals, but its importance in fish appears to be limited that so far seemed to belong to diabetic humans only. Several laboratories worldwide have made important efforts in order to better understand this strange phenotype observed in fish. However, the mechanism of carbohydrate/glucose metabolism is astonishingly complex. Read More

    Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle.
    BMC Genomics 2018 Apr 10;19(1):243. Epub 2018 Apr 10.
    The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK.
    Background: The potential of circulating miRNAs as biomarkers of tissue function, both in health and disease, has been extensively demonstrated in humans. In addition, circulating miRNA biomarkers offer significant potential towards improving the productivity of livestock species, however, such potential has been hampered by the absence of information on the nature and source of circulating miRNA populations in these species. In addition, many miRNAs originally proposed as robust biomarkers of a particular tissue or disease in humans have been later shown not to be tissue specific and thus to actually have limited biomarker utility. Read More

    MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae.
    BMC Genomics 2018 Apr 10;19(1):241. Epub 2018 Apr 10.
    Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway.
    Background: MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression at the post-transcriptional level and play a key role in the control of innate and adaptive immune responses. For a subclinical infection such as bovine streptococcal mastitis, early detection is a great challenge, and miRNA profiling could potentially assist in the diagnosis and contribute to the understanding of the pathogenicity and defense mechanisms. We have examined the miRNA repertoire and the transcript level of six key immune genes [tumor necrosis factor alpha (TNFα), interleukin-1 beta (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10) and transforming growth factor beta 1 (TGFβ1)] during the early phase response of bovine immature macrophages to in vitro infection with live Streptococcus agalactiae. Read More

    Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423.
    BMC Genomics 2018 Apr 10;19(1):242. Epub 2018 Apr 10.
    IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France.
    Background: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. Read More

    DNA methylation profiles correlated to striped bass sperm fertility.
    BMC Genomics 2018 Apr 10;19(1):244. Epub 2018 Apr 10.
    Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
    Background: Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Read More

    Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.
    BMC Genomics 2018 Apr 10;19(1):240. Epub 2018 Apr 10.
    Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
    Background: Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Read More

    Classification and phylogenetic analyses of the Arabidopsis and tomato G-type lectin receptor kinases.
    BMC Genomics 2018 Apr 6;19(1):239. Epub 2018 Apr 6.
    Department of Nematology, University of California, Riverside, California, USA.
    Background: Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While C-LecRKs are represented by one or two members in all plant species investigated and have unknown functions, L-LecRKs have been characterized in a few plant species and have been shown to play roles in plant defense against pathogens. Read More

    TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.
    BMC Genomics 2018 Apr 5;19(1):238. Epub 2018 Apr 5.
    Australian Regenerative Medicine Institute, Systems Biology Institute Australia, Monash University, Clayton, VIC, Australia.
    Background: A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57-74, 2012; Nat 507:462-70, 2014; Nat 507:455-61, 2014; Nat 518:317-30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. Read More

    Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils.
    BMC Genomics 2018 Apr 4;19(1):236. Epub 2018 Apr 4.
    Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Copenhagen, Denmark.
    Background: Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. Read More

    Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data.
    BMC Genomics 2018 Apr 4;19(1):235. Epub 2018 Apr 4.
    Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
    Background: Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce.

    Results: The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. Read More

    New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus).
    BMC Genomics 2018 Apr 4;19(1):233. Epub 2018 Apr 4.
    Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.
    Background: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Read More

    Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits.
    BMC Genomics 2018 Apr 5;19(1):237. Epub 2018 Apr 5.
    Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Building 80, 306 Carmody Road, Brisbane, St Lucia, QLD, 4072, Australia.
    Background: There are an exceedingly large number of sequence variants discovered through whole genome sequencing in most populations, including cattle. Deciphering which of these affect complex traits is a major challenge. In this study we hypothesize that variants in some functional classes, such as splice site regions, coding regions, DNA methylated regions and long noncoding RNA will explain more variance in complex traits than others. Read More

    The constitutive differential transcriptome of a brain circuit for vocal learning.
    BMC Genomics 2018 Apr 3;19(1):231. Epub 2018 Apr 3.
    Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA.
    Background: The ability to imitate the vocalizations of other organisms, a trait known as vocal learning, is shared by only a few organisms, including humans, where it subserves the acquisition of speech and language, and 3 groups of birds. In songbirds, vocal learning requires the coordinated activity of a set of specialized brain nuclei referred to as the song control system. Recent efforts have revealed some of the genes that are expressed in these vocal nuclei, however a thorough characterization of the transcriptional specializations of this system is still missing. Read More

    Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse.
    BMC Genomics 2018 Apr 3;19(1):232. Epub 2018 Apr 3.
    Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
    Background: Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. Read More

    A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus).
    BMC Genomics 2018 Apr 2;19(1):230. Epub 2018 Apr 2.
    State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
    Background: A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. Read More

    DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures.
    BMC Genomics 2018 Apr 2;19(1):229. Epub 2018 Apr 2.
    Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Naples, Italy.
    Background: In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability with direct effects on disease etiology as well as phenotypic and genotypic variations in evolutionary processes. To identify possible factors influencing inter-individual methylation variability, we studied methylation values standard deviation of 166 healthy individuals searching for possible associations with genomic features and evolutionary signatures. Read More

    RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages.
    BMC Genomics 2018 Apr 2;19(1):227. Epub 2018 Apr 2.
    Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012, Bern, Switzerland.
    Background: Trypanosoma brucei brucei, the parasite causing Nagana in domestic animals, is closely related to the parasites causing sleeping sickness, but does not infect humans. In addition to its importance as a pathogen, the relative ease of genetic manipulation and an innate capacity for RNAi extend its use as a model organism in cell and infection biology. During its development in its mammalian and insect (tsetse fly) hosts, T. Read More

    iTRAQ-based quantitative proteomic analysis reveals the lateral meristem developmental mechanism for branched spike development in tetraploid wheat (Triticum turgidum L.).
    BMC Genomics 2018 Apr 2;19(1):228. Epub 2018 Apr 2.
    College of Agronomy, National Key Laboratory of Crop Genetics and Germplasm Enhancement/JCIC-MCP, Nanjing Agricultural University, Nanjing, 210095, China.
    Background: Spike architecture mutants in tetraploid wheat (Triticum turgidum L., 2n = 28, AABB) have a distinct morphology, with parts of the rachis node producing lateral meristems that develop into ramified spikelete (RSs) or four-rowed spikelete (FRSs). The genetic basis of RSs and FRSs has been analyzed, but little is known about the underlying developmental mechanisms of the lateral meristem. Read More

    Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application.
    BMC Genomics 2018 03 21;19(Suppl 4):170. Epub 2018 Mar 21.
    Department of Electrical and Computer Engineering, University of California, Davis, 95616, CA, USA.
    Background: Genotype-phenotype association has been one of the long-standing problems in bioinformatics. Identifying both the marginal and epistatic effects among genetic markers, such as Single Nucleotide Polymorphisms (SNPs), has been extensively integrated in Genome-Wide Association Studies (GWAS) to help derive "causal" genetic risk factors and their interactions, which play critical roles in life and disease systems. Identifying "synergistic" interactions with respect to the outcome of interest can help accurate phenotypic prediction and understand the underlying mechanism of system behavior. Read More

    Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids.
    BMC Genomics 2018 03 21;19(Suppl 4):191. Epub 2018 Mar 21.
    Department of ECE, University of Texas at Austin, Austin, Texas, USA.
    Background: Haplotype assembly is the task of reconstructing haplotypes of an individual from a mixture of sequenced chromosome fragments. Haplotype information enables studies of the effects of genetic variations on an organism's phenotype. Most of the mathematical formulations of haplotype assembly are known to be NP-hard and haplotype assembly becomes even more challenging as the sequencing technology advances and the length of the paired-end reads and inserts increases. Read More

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